Check introns with unique specificities

Recheck list of risdi/brana-specific introns

Last updated: 2023-03-08

Checks: 6 1

Knit directory: 20211209_JingxinRNAseq/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(19900924)

The command set.seed(19900924) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 933025a

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 933025a. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.RData
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/20220707_TitrationSeries_DE_testing.nb.html
    Ignored:    code/.DS_Store
    Ignored:    code/._DOCK7.pdf
    Ignored:    code/._DOCK7_DMSO1.pdf
    Ignored:    code/._DOCK7_SM2_1.pdf
    Ignored:    code/._FKTN_DMSO_1.pdf
    Ignored:    code/._FKTN_SM2_1.pdf
    Ignored:    code/._MAPT.pdf
    Ignored:    code/._PKD1_DMSO_1.pdf
    Ignored:    code/._PKD1_SM2_1.pdf
    Ignored:    code/.snakemake/
    Ignored:    code/1KG_HighCoverageCalls.samplelist.txt
    Ignored:    code/5ssSeqs.tab
    Ignored:    code/Alignments/
    Ignored:    code/Branaplam_Risdiplam_specific_introns.bed.gz
    Ignored:    code/Branaplam_Risdiplam_specific_introns.bed.gz.tbi
    Ignored:    code/ChemCLIP/
    Ignored:    code/ClinVar/
    Ignored:    code/DE_testing/
    Ignored:    code/DE_tests.mat.counts.gz
    Ignored:    code/DE_tests.txt.gz
    Ignored:    code/DataNotToCommit/
    Ignored:    code/DoseResponseData/
    Ignored:    code/Fastq/
    Ignored:    code/FastqFastp/
    Ignored:    code/FragLenths/
    Ignored:    code/Meme/
    Ignored:    code/Multiqc/
    Ignored:    code/OMIM/
    Ignored:    code/OldBigWigs/
    Ignored:    code/PhyloP/
    Ignored:    code/QC/
    Ignored:    code/ReferenceGenomes/
    Ignored:    code/Session.vim
    Ignored:    code/Session2.vim
    Ignored:    code/SplicingAnalysis/
    Ignored:    code/TracksSession
    Ignored:    code/bigwigs/
    Ignored:    code/featureCounts/
    Ignored:    code/figs/
    Ignored:    code/geena/
    Ignored:    code/hg38ToMm39.over.chain.gz
    Ignored:    code/igv_session.template.xml
    Ignored:    code/igv_session.xml
    Ignored:    code/log
    Ignored:    code/logs/
    Ignored:    code/rstudio-server.job
    Ignored:    code/scratch/
    Ignored:    code/test.txt.gz
    Ignored:    code/testPlottingWithMyScript.ForJingxin.sh
    Ignored:    code/testPlottingWithMyScript.ForJingxin2.sh
    Ignored:    code/testPlottingWithMyScript.ForJingxin3.sh
    Ignored:    code/testPlottingWithMyScript.ForJingxin4.sh
    Ignored:    code/testPlottingWithMyScript.sh
    Ignored:    code/tracks.xml
    Ignored:    data/~$52CompoundsTempPlateLayoutForPipettingConvenience.xlsx
    Ignored:    output/._PioritizedIntronTargets.pdf

Unstaged changes:
    Modified:   analysis/20230306_CheckIntronsWithUniqueSpecifities.Rmd
    Modified:   code/scripts/GenometracksByGenotype

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/20230306_CheckIntronsWithUniqueSpecifities.Rmd) and HTML (docs/20230306_CheckIntronsWithUniqueSpecifities.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	933025a	Benjmain Fair	2023-03-07	update nb
html	933025a	Benjmain Fair	2023-03-07	update nb
Rmd	c2a4a84	Benjmain Fair	2023-03-07	update screenshot nb
html	c2a4a84	Benjmain Fair	2023-03-07	update screenshot nb
Rmd	ea36e65	Benjmain Fair	2023-03-07	added igv session
html	ea36e65	Benjmain Fair	2023-03-07	added igv session

knitr::opts_chunk$set(echo = TRUE, warning = F, message = F)

library(tidyverse)

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──

✔ ggplot2 3.3.6     ✔ purrr   0.3.4
✔ tibble  3.1.7     ✔ dplyr   1.0.9
✔ tidyr   1.2.0     ✔ stringr 1.4.0
✔ readr   2.1.2     ✔ forcats 0.5.1

── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Recheck list of risdi/brana-specific introns

I previously made a list of risdiplam/branaplam/C2C5-specific introns based on the dose response experiment. Because the different molecules have different genome-wide effective potencies (ie, 100nM C2C5 is different than 100nM risdiplam, despite them having generally similar specificity profiles), I tested for a difference in the EC50 of each intron for each traitment pair, relative to the genome-wide median. You can see that in a previous notebook I plotted the dose-response datapoints for a random sample of 20 of these significant molecule-specific effects, and they are generally believable effects from those.

GA.GT.Introns <- read_tsv("../output/EC50Estimtes.FromPSI.txt.gz")

ColorKey <- c("Branaplam-specific"="#005A32", "Risdiplam-specific"="#084594", "Non significant"="#969696")

P1.dat <- GA.GT.Introns %>%
  mutate(Color = case_when(
    EC.Ratio.Test.Estimate.FDR_Branaplam.Risdiplam > 0.05 ~ "Non significant",
    ECRatio.ComparedToGenomewideMedian_Branaplam.Risdiplam > 1 ~ "Risdiplam-specific",
    ECRatio.ComparedToGenomewideMedian_Branaplam.Risdiplam < 1 ~ "Branaplam-specific"
  ))

ggplot(P1.dat, aes(x=ED50_Branaplam, y=ED50_Risdiplam, color=Color)) +
  geom_point() +
  scale_x_continuous(trans='log10', limits = c(1, 1E7)) +
  scale_y_continuous(trans='log10', limits = c(1, 1E7)) +
  scale_color_manual(values=ColorKey) +
  labs(x= "Branaplam\nED50 (nanomolar)", y= "Risdiplam\nED50 (nanomolar)", color=NULL) +
  theme(legend.position='bottom') +
  theme_bw()

Version	Author	Date
ea36e65	Benjmain Fair	2023-03-07

P1.dat %>%
  count(Color)

# A tibble: 4 × 2
  Color                  n
  <chr>              <int>
1 Branaplam-specific   240
2 Non significant      200
3 Risdiplam-specific   161
4 <NA>                2878

Ok, so each point is a branaplam-specific or risdiplam-specific GA-GT intron. There are 200 non-significant points, 161 risdiplam-specific points, and 240 branaplam-specific points. I think it will be useful for Jingxin to be able to easily visualize these before validating them… Some introns that change PSI from 1% to 3% might be very significant, but not the best for validation. Furthermore, not all of these events might be involved in poison exon inclusion. Some of them might just be alt 5’ss or something. And these details might inform which are the best candidates for validation by flanking PCR primers. Also, when looking at the data, some of the ‘risdiplam-specific’ introns I called are just not believable effects. Like the dose-response data points might just be too noisy. I did a reasonable job of filtering these out, and trying to make the FDR estimate reasonably calibrated… Or like there are some examples where it appears ‘risdiplam-specific’ but it is because the cryptic event is only just barely visible at the highest dose of risdiplam, and not visible in any of the branaplam doses (so it just requires a really really high dose to see the effect). So for all these reasons, it will be best to check the raw coverage data first… So I’ll write the out this list as a bedfile for easy viewing in IGV, a save a session that has the bedfile loaded, along with bigwigs for the dose response experiment so hopefully it will be easy to view.

P1.dat %>%
  dplyr::select(chrom=`#Chrom`, start, end, junc, score=ECRatio.ComparedToGenomewideMedian_Branaplam.Risdiplam, strand=strand.y, Color) %>%
  filter(!is.na(score)) %>%
  mutate(thickStart = start, thickEnd=end, Color=recode(Color, !!!ColorKey)) %>%
  mutate(RgbCol = apply(col2rgb(Color), 2, paste, collapse=',')) %>%
  dplyr::select(chrom:strand, thickStart, thickEnd, RgbCol) %>%
  arrange(chrom, start, end) %>%
  write_tsv("../code/Branaplam_Risdiplam_specific_introns.bed", col_names = F)

bgzip ../code/Branaplam_Risdiplam_specific_introns.bed
tabix -p bed ../code/Branaplam_Risdiplam_specific_introns.bed.gz

So to view, you will need to use the globus link I shared with Jingxin to download the code directory, or at minimum download the code/bigwigs folder of bigwig files, the code/tracks.xml IGV session, and the code/Branaplam_Risdiplam_specific_introns.bed.gz and code/Branaplam_Risdiplam_specific_introns.bed.gz.tbi. Then, from IGV, go to File >> OpenSession and open the tracks.xml. The tracks.xml uses relative filepaths so you need to preserve the relative filepaths of the thing you downloaded (that is, they need to all be in the same folder, such as a folder named code).

Now you should be able to select the Branaplam_Risdiplam_specific_introns.bed track, and Ctl-F or Ctl-B to jump to the next GA-GT introns, colored according to significance. Browse around to find coordinates of potential splice events for validation. Note that each bigwig is already normalized signal relative to library depth. With autoscaling for the y-axis turned on (the default), it may be visually obvious to see the poison exons, but it might not be totally obvious to see if there are effects on gene expression. To better visualize effects on host gene expression, I recommend just selecting all bigwig tracks and right-click to “group autoscale”. Since coverage of each track is already normalized by library size, it should be easy to visually interpret if there is a change in gene expression.

Here are screenshots of a few examples…

BranaSpecific1

BranaSpecific2

RisdiSpecific1

In general, I’m noticing there a quite a few believable branaplam-specific examples but the risdlam-specific are for the most part very small specificity effect sizes. That is, there are very few obviously risdiplam-specific events, compared to branaplam-specific events.

Let’s list the top risdi-specific introns in the following table:

P1.dat %>%
  arrange(desc(ECRatio.ComparedToGenomewideMedian_Branaplam.Risdiplam)) %>%
  head() %>%
  knitr::kable()

junc	#Chrom	start	end	gid	strand.y	seq	Donor.score	gene_names	gene_ids	SpliceDonor	UpstreamSpliceAcceptor	IntronType	Steepness	LowerLimit	UpperLimit	ED50_Branaplam	ED50_C2C5	ED50_Risdiplam	spearman.coef.Branaplam	spearman.coef.C2C5	spearman.coef.Risdiplam	EC.Ratio.Test.Estimate_Branaplam.C2C5	EC.Ratio.Test.Estimate_Branaplam.Risdiplam	EC.Ratio.Test.Estimate_C2C5.Risdiplam	ECRatio.ComparedToGenomewideMedian_Branaplam.C2C5	ECRatio.ComparedToGenomewideMedian_Branaplam.Risdiplam	ECRatio.ComparedToGenomewideMedian_C2C5.Risdiplam	EC.Ratio.Test.Estimate.P_Branaplam.C2C5	EC.Ratio.Test.Estimate.P_Branaplam.Risdiplam	EC.Ratio.Test.Estimate.P_C2C5.Risdiplam	EC.Ratio.Test.Estimate.FDR_Branaplam.C2C5	EC.Ratio.Test.Estimate.FDR_Branaplam.Risdiplam	EC.Ratio.Test.Estimate.FDR_C2C5.Risdiplam	Color
chr2:72179461:72182894:clu_4568_-	chr2	72179461	72182894	chr2_clu_4568_-	-	GAGAGTAAGTA	6.005894	EXOC6B	ENSG00000144036.16	chr2.72182894.-	chr2.72182903.-	Annotated	-2.7570544	3.1361062	31.384932	2.495499e+09	248.12468	785.0629479	0.2277339	0.5594024	0.9139077	1.005744e+07	3178724.1044	0.3160571	7.482724e+06	25547101.480	3.0610287	0.0000000	0.0000000	0.0000000	0.0000000	0.0000000	0.0000000	Risdiplam-specific
chr13:20404741:20405904:clu_25569_-	chr13	20404741	20405904	chr13_clu_25569_-	-	GAGAGTAAGTC	5.446634	CRYL1	ENSG00000165475.15	chr13.20405904.-	chr13.20405997.-	Alt 5’ss	-2.8191629	3.3431713	48.302244	1.641993e+09	1400.00395	4071.6117233	0.1740777	0.6024948	0.9128709	1.172849e+06	403278.4047	0.3438452	8.725985e+05	3241109.952	3.3301579	0.0000000	0.0000000	0.0000000	0.0000000	0.0000000	0.0000000	Risdiplam-specific
chr9:108931201:108933271:clu_18237_-	chr9	108931201	108933271	chr9_clu_18237_-	-	AAGAGTAAGCA	4.905988	ELP1	ENSG00000070061.15	chr9.108933271.-	chr9.108933405.-	Alt 5’ss	-9.6753286	0.5638888	7.339398	2.540583e+07	33.32162	895.8671341	0.1926687	0.9052038	0.7822166	7.624427e+05	28358.9229	0.0371948	5.672567e+05	227917.950	0.3602338	0.0000021	0.0000000	0.0000000	0.0000023	0.0000000	0.0000000	Risdiplam-specific
chr18:10773629:10774006:clu_33760_-	chr18	10773629	10774006	chr18_clu_33760_-	-	ATGAGTAAGTC	4.559120	PIEZO2	ENSG00000154864.12	chr18.10774006.-	chr18.10774036.-	Annotated	-2.2089456	0.0687500	51.453519	1.001587e+07	143.33677	1424.8728605	0.2738613	0.9128709	0.8416254	6.987650e+04	7029.3086	0.1005962	5.198805e+04	56493.880	0.9742791	0.0000000	0.0000000	0.4229854	0.0000000	0.0000000	0.6497405	Risdiplam-specific
chr19:10330526:10332870:clu_34319_-	chr19	10330526	10332870	chr19_clu_34319_-	-	GAGAGTACGCC	2.214523	RAVER1	ENSG00000161847.14	chr19.10332870.-	chr19.10332909.-	Alt 5’ss	-0.0000251	0.1685537	3.589164	1.413434e+03	22.81686	0.7759248	0.9831921	-0.2712254	-0.5135291	6.194690e+01	1821.6118	29.4060210	4.608844e+01	14640.120	284.7988165	0.9969948	0.9965823	0.9983501	0.4873920	0.4546814	1.0000000	Non significant
chr4:41014398:41032584:clu_10225_-	chr4	41014398	41032584	chr4_clu_10225_-	-	AGGAGTAGGTG	5.043083	APBB2	ENSG00000163697.17	chr4.41032584.-	chr4.41032626.-	Alt 5’ss	-3.0030040	0.0355949	1.682290	3.820296e+05	22.66113	452.1565311	0.3195048	0.8580987	0.9082951	1.685837e+04	844.9056	0.0501179	1.254261e+04	6790.426	0.4853942	0.0010952	0.0000000	0.0006567	0.0009786	0.0000000	0.0025582	Risdiplam-specific

After looking at some of the top risdiplam-specific hits from the list above, here is perhaps the most clear example:

RisdiSpecific2

Let’s do some exploring of the data a bit more to see if there are any introns and interesting host genes with reasonable differences in specificity between the risdiplam and branaplam treatments. So like HTT should show up here for example, but I wonder what other interesting genes may be on the list.

ColorKey <- c("Branaplam-specific"="#005A32", "Risdiplam-specific"="#084594", "Non significant"="#969696")


P.histogram <- P1.dat %>%
  mutate(Color = factor(Color, levels=names(ColorKey))) %>%
  ggplot(aes(x=log2(ECRatio.ComparedToGenomewideMedian_Branaplam.Risdiplam), fill=Color)) +
  geom_histogram() +
  scale_fill_manual(values=ColorKey) +
  theme(legend.position="bottom") +
  labs(x="Specificity\nlog2(BranaplamEC50/RisdiplamEC50)", caption="EC50s normalized to median before comparing ratios")

P.histogram

Let’s just consider stronger specificity effects, with abs(log2 ratio) > 2.

Note that I haven’t filtered these GA-GT intron affects for those with effects on the host gene. So like some of these hits may not effect host gene expression.

P.histogram +
  xlim(c(-10, 10)) +
  geom_vline(xintercept=c(-2,2))

SpecificEffects <- P1.dat %>%
  mutate(log2Ratio = log2(ECRatio.ComparedToGenomewideMedian_Branaplam.Risdiplam)) %>%
  filter(abs(log2Ratio)>2) %>%
  filter(!Color == "Non significant") %>%
  separate_rows(gene_names, gene_ids, sep=',') %>%
  dplyr::select(Color, log2Ratio, gene_names, gene_ids) %>%
  # filter(gene_names == "HTT") %>%
  arrange(log2Ratio)

head(SpecificEffects)

# A tibble: 6 × 4
  Color              log2Ratio gene_names gene_ids          
  <chr>                  <dbl> <chr>      <chr>             
1 Branaplam-specific    -30.8  ASB3       ENSG00000115239.24
2 Branaplam-specific    -15.7  SETD5      ENSG00000168137.18
3 Branaplam-specific     -8.13 C8orf88    ENSG00000253250.3 
4 Branaplam-specific     -7.52 NCF2       ENSG00000116701.15
5 Branaplam-specific     -7.16 ANKRD10    ENSG00000088448.14
6 Branaplam-specific     -6.67 DAPP1      ENSG00000070190.13

Let’s also merge this with some gene expression data. For convenience, I’m just going to merge it with the spearman of the dose:response effect on expression, and also gather the FoldChange at the mid-point dose, which I think is a reasonable place to start to see some effects (the high dose in this experiment might be a bit ridiculous from the pharmacology point of view).

GeneExpressionData.tidy <- read_tsv("../code/DoseResponseData/LCL/TidyExpressionDoseData.txt.gz") %>%
  mutate(CPM = log2(CPM))

As a data parsing side note… I can quickly get the doses for the midpoint doses by filtering on the color column. Let me remember how I coded the colors to get the appropriate doses

GeneExpressionData.tidy %>%
  distinct(color, .keep_all=T) %>%
  ggplot(aes(x=1, y=color, fill=color)) +
  geom_raster() +
  geom_label(aes(label=color)) +
  scale_fill_identity() +
  facet_wrap(~treatment)

Ok, so in other words, I want to filter for color = #969696 (DMSO), or #74C476 (middle branaplam dose), or #6BAED6 (middle risdiplam dose).

MoleculeSpecificEffects <- GeneExpressionData.tidy %>%
  filter(color %in% c("#74C476", "#6BAED6")) %>%
  filter(Geneid %in% SpecificEffects$gene_ids) %>%
  dplyr::select(Geneid, CPM, SampleName, treatment, spearman) %>%
  left_join(
    GeneExpressionData.tidy %>%
      filter(color %in% c("#969696")) %>%
      filter(Geneid %in% SpecificEffects$gene_ids) %>%
      dplyr::select(Geneid, CPM) %>%
      group_by(Geneid) %>%
      summarise(CPM_DMSO = mean(CPM))
  ) %>%
  mutate(Log2FoldChange = CPM - CPM_DMSO) %>%
  pivot_wider(names_from = c("treatment"), values_from=c("CPM", "spearman", "SampleName", "Log2FoldChange")) %>%
  inner_join(SpecificEffects, by=c("Geneid"="gene_ids")) %>%
  dplyr::rename(log2RatioOfSplicingED50= log2Ratio) %>%
  arrange(log2RatioOfSplicingED50)

MoleculeSpecificEffects %>%
  filter(gene_names == "HTT") %>%
  knitr::kable()

Geneid	CPM_DMSO	CPM_Branaplam	CPM_Risdiplam	spearman_Branaplam	spearman_Risdiplam	SampleName_Branaplam	SampleName_Risdiplam	Log2FoldChange_Branaplam	Log2FoldChange_Risdiplam	Color	log2RatioOfSplicingED50	gene_names
ENSG00000197386.12	7.892803	4.910666	7.186162	-0.8333333	-0.8666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-2.982138	-0.7066416	Branaplam-specific	-3.346746	HTT

Ok that makes sense. Note that the CPM columns are actually log2CPM. We can see that HTT has a branaplam-specific effect. Let’s print the full table…

MoleculeSpecificEffects %>%
  knitr::kable()

Geneid	CPM_DMSO	CPM_Branaplam	CPM_Risdiplam	spearman_Branaplam	spearman_Risdiplam	SampleName_Branaplam	SampleName_Risdiplam	Log2FoldChange_Branaplam	Log2FoldChange_Risdiplam	Color	log2RatioOfSplicingED50	gene_names
ENSG00000115239.24	4.3081982	4.1890728	4.3196633	-0.8166667	0.9000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1191255	0.0114651	Branaplam-specific	-30.837171	ASB3
ENSG00000168137.18	6.0661148	6.1276722	6.2102237	-0.0166667	0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0615575	0.1441089	Branaplam-specific	-15.702685	SETD5
ENSG00000253250.3	2.5719371	2.9005508	2.5340035	0.8000000	0.5166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.3286136	-0.0379337	Branaplam-specific	-8.128940	C8orf88
ENSG00000116701.15	5.4192338	5.5229186	5.5790500	-0.4000000	-0.1333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1036848	0.1598162	Branaplam-specific	-7.515091	NCF2
ENSG00000088448.14	5.0353703	4.9280315	5.1069535	-0.2500000	0.8000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1073388	0.0715831	Branaplam-specific	-7.155299	ANKRD10
ENSG00000070190.13	5.7763049	4.3533232	3.9080913	-0.9666667	-0.9000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.4229816	-1.8682135	Branaplam-specific	-6.669824	DAPP1
ENSG00000050748.17	5.2584252	5.3263748	5.3632371	-0.5333333	0.5500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0679496	0.1048119	Branaplam-specific	-6.577305	MAPK9
ENSG00000196792.12	3.7273769	4.0174847	4.0453431	0.9500000	0.8833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2901078	0.3179662	Branaplam-specific	-6.202894	STRN3
ENSG00000170476.16	8.4436025	8.1173012	8.3130122	-1.0000000	-0.9500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3263014	-0.1305903	Branaplam-specific	-5.524008	MZB1
ENSG00000064933.18	4.6810344	2.2646238	2.5518368	-0.9833333	-1.0000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-2.4164106	-2.1291976	Branaplam-specific	-5.522988	PMS1
ENSG00000087460.25	10.2499857	10.0997995	10.1649180	-0.9333333	-0.9166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1501862	-0.0850677	Branaplam-specific	-4.958655	GNAS
ENSG00000180198.16	7.0524244	9.6440401	7.2642243	0.9833333	0.9166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	2.5916157	0.2117999	Branaplam-specific	-4.819941	RCC1
ENSG00000242125.3	4.9287895	3.2413027	4.5095734	-0.9833333	-0.9666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.6874868	-0.4192161	Branaplam-specific	-4.819941	SNHG3
ENSG00000112739.17	6.2932301	6.3802628	6.2891568	-0.4333333	-0.2333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0870327	-0.0040733	Branaplam-specific	-4.813817	PRPF4B
ENSG00000205861.12	0.9774978	1.2937702	0.5553771	-0.1833333	-0.7500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.3162724	-0.4221207	Branaplam-specific	-4.744962	PCOTH
ENSG00000131981.16	5.6559843	5.6235088	5.7031307	0.2333333	0.7666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0324755	0.0471464	Branaplam-specific	-4.693610	LGALS3
ENSG00000078747.15	6.1734625	5.7468173	6.1599485	-0.8666667	-0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4266451	-0.0135139	Branaplam-specific	-4.614054	ITCH
ENSG00000258724.1	-Inf	-6.1574410	-Inf	-0.1980295	0.2738613	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	Inf	NaN	Branaplam-specific	-4.608812	PINX1
ENSG00000254093.9	3.9415665	3.6255573	3.8983668	-0.9833333	-0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3160092	-0.0431996	Branaplam-specific	-4.608812	PINX1
ENSG00000143569.19	7.7077429	7.2917077	7.0205834	-0.8666667	-0.9500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4160352	-0.6871596	Branaplam-specific	-4.586487	UBAP2L
ENSG00000102921.8	6.1395411	6.0907831	6.1279102	0.3666667	0.0666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0487579	-0.0116309	Branaplam-specific	-4.428989	N4BP1
ENSG00000100368.14	3.9931320	3.6222784	3.9677602	-0.9000000	-0.3833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3708536	-0.0253719	Branaplam-specific	-4.411832	CSF2RB
ENSG00000111237.19	5.9226823	5.1901804	5.8840081	-1.0000000	-0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.7325019	-0.0386742	Branaplam-specific	-4.338322	VPS29
ENSG00000172175.15	6.6152367	6.9167005	6.7481051	-0.1333333	0.3833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.3014638	0.1328683	Branaplam-specific	-4.278250	MALT1
ENSG00000010270.13	5.7620132	5.9089846	5.7548570	0.9333333	0.8333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1469714	-0.0071562	Branaplam-specific	-4.248940	STARD3NL
ENSG00000090372.15	6.0804844	4.2989135	5.9960428	-0.9333333	-0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.7815710	-0.0844417	Branaplam-specific	-4.199628	STRN4
ENSG00000176531.10	3.2001713	3.5516429	3.4279162	0.9000000	0.8000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.3514715	0.2277449	Branaplam-specific	-4.154132	PHLDB3
ENSG00000000938.13	5.4668031	4.9207099	5.3181011	-0.5000000	-0.5000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.5460932	-0.1487020	Branaplam-specific	-3.990816	FGR
ENSG00000147905.17	5.5084515	5.2834282	5.3798056	-0.9500000	-0.2333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2250233	-0.1286460	Branaplam-specific	-3.951407	ZCCHC7
ENSG00000153914.16	5.3992150	3.2561870	5.0795539	-0.8833333	-0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-2.1430280	-0.3196611	Branaplam-specific	-3.940037	SREK1
ENSG00000101639.18	4.9258571	5.0520124	4.8327785	-0.4333333	-0.8166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1261553	-0.0930786	Branaplam-specific	-3.934320	CEP192
ENSG00000163960.12	5.5158041	5.7377556	5.6465791	0.5666667	0.4500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2219515	0.1307750	Branaplam-specific	-3.872331	UBXN7
ENSG00000106268.15	4.9628095	5.2294993	5.0653461	0.4833333	-0.5833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2666898	0.1025367	Branaplam-specific	-3.805406	NUDT1
ENSG00000102897.10	4.5736910	4.8807922	4.4613245	-0.1500000	-0.0500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.3071011	-0.1123666	Branaplam-specific	-3.734031	LYRM1
ENSG00000110090.13	4.8495802	5.0761787	4.9416200	0.4666667	0.5333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2265985	0.0920398	Branaplam-specific	-3.648140	CPT1A
ENSG00000134882.16	5.1507778	4.3414083	4.6378393	-0.9833333	-0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.8093695	-0.5129385	Branaplam-specific	-3.622183	UBAC2
ENSG00000171530.14	6.4857089	5.8097853	6.3302933	-0.9666667	-0.3833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.6759236	-0.1554156	Branaplam-specific	-3.621325	TBCA
ENSG00000147439.13	5.1520551	5.0749800	5.0856878	-0.8833333	0.4833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0770752	-0.0663673	Branaplam-specific	-3.615688	BIN3
ENSG00000177565.18	5.4283368	5.4312737	5.6095957	-0.6666667	0.1000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0029369	0.1812589	Branaplam-specific	-3.588868	TBL1XR1
ENSG00000064313.12	5.4381021	4.5840260	4.3196633	-0.8000000	-0.9000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.8540761	-1.1184388	Branaplam-specific	-3.576764	TAF2
ENSG00000167491.17	6.6118164	6.6513222	6.6583563	-0.7166667	0.5000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0395057	0.0465399	Branaplam-specific	-3.547966	GATAD2A
ENSG00000080845.17	5.4454116	5.1250684	5.3773074	-0.8166667	0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3203432	-0.0681042	Branaplam-specific	-3.535267	DLGAP4
ENSG00000151233.11	4.0694815	2.9167005	4.0148087	-0.9833333	-0.6833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.1527810	-0.0546728	Branaplam-specific	-3.487187	GXYLT1
ENSG00000139116.18	5.2251809	5.1192651	5.2784859	-0.7166667	-0.5000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1059158	0.0533050	Branaplam-specific	-3.473336	KIF21A
ENSG00000108061.12	6.6597812	6.5503495	6.4688532	0.0666667	-0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1094316	-0.1909279	Branaplam-specific	-3.422720	SHOC2
ENSG00000130475.14	4.8883909	4.7554484	4.8709263	-0.9833333	0.3000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1329426	-0.0174646	Branaplam-specific	-3.391896	FCHO1
ENSG00000166974.13	5.3297854	5.5865519	5.3556426	-0.1500000	0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2567665	0.0258572	Branaplam-specific	-3.348989	MAPRE2
ENSG00000197386.12	7.8928033	4.9106655	7.1861617	-0.8333333	-0.8666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-2.9821378	-0.7066416	Branaplam-specific	-3.346746	HTT
ENSG00000127554.13	4.9440687	4.9929410	5.0031897	-0.6666667	0.3333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0488723	0.0591209	Branaplam-specific	-3.315597	GFER
ENSG00000180901.11	5.3235507	5.3641595	5.4693225	-0.5833333	0.4500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0406088	0.1457718	Branaplam-specific	-3.297018	KCTD2
ENSG00000132394.11	4.7444785	4.9776270	4.9637693	-0.4666667	-0.2333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2331485	0.2192908	Branaplam-specific	-3.285066	EEFSEC
ENSG00000107263.18	7.7481426	8.0216906	7.9613528	0.9333333	0.9666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2735480	0.2132102	Branaplam-specific	-3.249082	RAPGEF1
ENSG00000135363.12	4.3804710	4.2886085	4.4726029	-0.3166667	-0.0333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0918626	0.0921319	Branaplam-specific	-3.238942	LMO2
ENSG00000156642.17	5.8592412	5.9143566	5.8188535	0.9000000	0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0551154	-0.0403877	Branaplam-specific	-3.206832	NPTN
ENSG00000126581.13	6.1942389	6.4487329	6.2525491	0.9833333	0.8333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2544940	0.0583102	Branaplam-specific	-3.183238	BECN1
ENSG00000196843.17	6.6276038	6.6349427	6.6359595	-0.0166667	0.5666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0073389	0.0083558	Branaplam-specific	-3.167849	ARID5A
ENSG00000285733.1	-Inf	-Inf	-Inf	NA	NA	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	NaN	Branaplam-specific	-3.141239	AL031315.1
ENSG00000184465.16	0.7275724	0.3019907	0.5411633	-0.9166667	-0.5166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4255818	-0.1864092	Branaplam-specific	-3.141239	WDR27
ENSG00000100281.14	4.6081853	4.5670729	4.6862757	-0.8333333	-0.6000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0411124	0.0780904	Branaplam-specific	-3.090861	HMGXB4
ENSG00000136732.16	6.2975339	6.1987359	6.1234450	-0.8500000	-0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0987981	-0.1740889	Branaplam-specific	-3.077982	GYPC
ENSG00000126773.13	5.1310343	5.0410041	5.1415178	0.1500000	0.6833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0900302	0.0104835	Branaplam-specific	-3.013184	PCNX4
ENSG00000204899.6	4.8599721	4.6337219	4.8393279	-0.9333333	-0.6833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2262502	-0.0206442	Branaplam-specific	-2.991499	MZT1
ENSG00000163875.15	5.4606052	5.3918624	5.4006212	-0.7833333	0.4833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0687428	-0.0599841	Branaplam-specific	-2.964981	MEAF6
ENSG00000116473.14	7.6765605	7.6621394	7.5971973	-0.4500000	-0.8666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0144210	-0.0793632	Branaplam-specific	-2.956315	RAP1A
ENSG00000106028.11	6.8109793	6.0446829	6.7728359	-0.9333333	-0.7500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.7662965	-0.0381434	Branaplam-specific	-2.948600	SSBP1
ENSG00000278845.5	6.0796456	6.1821307	6.0841568	0.9166667	0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1024851	0.0045111	Branaplam-specific	-2.928467	MRPL45
ENSG00000175220.12	5.6868493	5.2503579	5.8641623	-0.9000000	-0.2333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4364914	0.1773130	Branaplam-specific	-2.885549	ARHGAP1
ENSG00000113558.19	6.6634023	6.1644871	6.6943265	-0.9833333	-0.3333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4989152	0.0309241	Branaplam-specific	-2.876467	SKP1
ENSG00000272772.1	-Inf	-Inf	-5.1170482	-0.1369306	-0.1460593	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	Inf	Branaplam-specific	-2.876467	AC104109.3
ENSG00000138185.20	7.9964849	8.0054224	7.9008041	-0.3500000	-0.1500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0089375	-0.0956808	Branaplam-specific	-2.835834	ENTPD1
ENSG00000118454.13	4.8260367	4.6132229	4.9503861	-0.9500000	0.1166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2128138	0.1243494	Branaplam-specific	-2.807663	ANKRD13C
ENSG00000165025.15	7.1479192	7.0854354	7.2593485	-0.9666667	-0.5333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0624838	0.1114293	Branaplam-specific	-2.803027	SYK
ENSG00000126653.18	4.8593663	4.6659263	4.8114702	-0.9166667	0.4333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1934400	-0.0478962	Branaplam-specific	-2.798763	NSRP1
ENSG00000065150.21	8.3889944	8.4050400	8.3266076	-0.4166667	-0.7166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0160456	-0.0623867	Branaplam-specific	-2.785237	IPO5
ENSG00000197150.12	5.2848027	4.8937680	5.4143332	-0.9000000	0.4500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3910347	0.1295306	Branaplam-specific	-2.783347	ABCB8
ENSG00000117419.16	5.3792829	5.4247010	5.3474975	-0.6666667	0.1333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0454181	-0.0317854	Branaplam-specific	-2.762573	ERI3
ENSG00000112851.14	6.0480217	5.4251715	6.1021203	-0.9333333	-0.5666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.6228502	0.0540986	Branaplam-specific	-2.751726	ERBIN
ENSG00000139826.6	4.2150254	4.1879643	4.1141730	-0.6833333	0.5166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0270611	-0.1008524	Branaplam-specific	-2.748700	ABHD13
ENSG00000130818.12	2.6949993	3.2434385	2.7686482	0.9166667	0.7500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.5484392	0.0736488	Branaplam-specific	-2.737337	ZNF426
ENSG00000197329.12	5.5318634	5.2577726	5.5384825	0.1500000	0.6000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2740908	0.0066191	Branaplam-specific	-2.734313	PELI1
ENSG00000170627.11	4.8964738	3.2305763	4.4556520	-0.9500000	-0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.6658975	-0.4408218	Branaplam-specific	-2.732351	GTSF1
ENSG00000125991.19	7.2077209	7.2163758	7.2842313	0.6500000	0.8000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0086549	0.0765104	Branaplam-specific	-2.711622	ERGIC3
ENSG00000070882.13	5.1022965	5.0162362	5.1308793	-0.8500000	-0.2833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0860603	0.0285828	Branaplam-specific	-2.711605	OSBPL3
ENSG00000082146.13	4.0901520	4.3404109	4.0850756	-0.4166667	0.2666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2502589	-0.0050764	Branaplam-specific	-2.667072	STRADB
ENSG00000101109.12	7.1971436	7.1499022	7.3565307	0.2500000	0.5166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0472414	0.1593871	Branaplam-specific	-2.666348	STK4
ENSG00000197150.12	5.2848027	4.8937680	5.4143332	-0.9000000	0.4500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3910347	0.1295306	Branaplam-specific	-2.631513	ABCB8
ENSG00000100852.13	4.0440229	4.2487641	4.1201617	0.2333333	0.4666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2047412	0.0761389	Branaplam-specific	-2.547770	ARHGAP5
ENSG00000060237.17	7.9237791	8.0417713	8.0869115	-0.7166667	0.5333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1179922	0.1631324	Branaplam-specific	-2.540969	WNK1
ENSG00000180628.15	6.6337140	6.8000239	6.7122781	0.8333333	0.6166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1663099	0.0785641	Branaplam-specific	-2.539899	PCGF5
ENSG00000120029.13	5.5698725	5.5713299	5.5790500	-0.6833333	-0.5833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0014574	0.0091774	Branaplam-specific	-2.535363	ARMH3
ENSG00000185009.12	6.6747080	6.5325570	6.6298859	-0.9000000	-0.5833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1421510	-0.0448221	Branaplam-specific	-2.534809	AP3M1
ENSG00000106785.15	6.4574479	6.0040059	6.5449525	-0.9833333	0.8333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4534420	0.0875046	Branaplam-specific	-2.522308	TRIM14
ENSG00000170627.11	4.8964738	3.2305763	4.4556520	-0.9500000	-0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.6658975	-0.4408218	Branaplam-specific	-2.494362	GTSF1
ENSG00000182628.13	5.7537633	5.5277458	5.6078919	-0.9500000	-0.8333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2260175	-0.1458715	Branaplam-specific	-2.465174	SKA2
ENSG00000116212.15	5.1342687	5.1684266	5.0390349	-0.5500000	-0.8833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0341580	-0.0952338	Branaplam-specific	-2.458638	LRRC42
ENSG00000154511.12	5.1856157	4.8842182	4.9868952	-0.9833333	-0.7666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3013975	-0.1987205	Branaplam-specific	-2.435005	DIPK1A
ENSG00000100979.15	3.3330269	3.2667253	3.2048799	0.6500000	0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0663015	-0.1281470	Branaplam-specific	-2.429309	PLTP
ENSG00000116353.16	4.2802065	3.8425590	4.3165372	-0.9000000	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4376474	0.0363308	Branaplam-specific	-2.415464	MECR
ENSG00000165406.16	5.7545129	5.8927478	5.8762440	-0.4333333	0.8833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1382349	0.1217311	Branaplam-specific	-2.413024	MARCHF8
ENSG00000115084.15	3.5913508	3.6849094	3.9341607	-0.6166667	0.4666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0935586	0.3428099	Branaplam-specific	-2.381796	SLC35F5
ENSG00000178397.13	-Inf	-Inf	-6.1170482	NA	0.1369306	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	Inf	Branaplam-specific	-2.381226	FAM220A
ENSG00000286075.1	-Inf	-Inf	-Inf	NA	NA	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	NaN	Branaplam-specific	-2.381226	AC009412.1
ENSG00000147586.10	3.5316801	3.5007705	3.6692214	-0.7833333	-0.8500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0309096	0.1375413	Branaplam-specific	-2.342313	MRPS28
ENSG00000276418.5	-Inf	-6.1574410	-4.5320857	0.4500000	-0.3333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	Inf	Inf	Branaplam-specific	-2.342313	AC036214.3
ENSG00000196295.12	1.7486049	1.5840260	1.9436477	-0.9333333	0.3166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1645788	0.1950428	Branaplam-specific	-2.297164	GARS1-DT
ENSG00000008018.9	7.6105603	6.4940593	7.6388825	-0.9833333	-0.1833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.1165011	0.0283222	Branaplam-specific	-2.280594	PSMB1
ENSG00000181007.9	1.9254386	2.3019907	1.8885763	0.8500000	0.8833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.3765520	-0.0368623	Branaplam-specific	-2.275857	ZFP82
ENSG00000064652.11	1.3213263	1.2604116	1.4679143	-0.4333333	0.1500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0609147	0.1465880	Branaplam-specific	-2.260318	SNX24
ENSG00000141068.14	5.8475194	6.0987677	6.1482738	0.6333333	0.3666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2512483	0.3007544	Branaplam-specific	-2.252941	KSR1
ENSG00000189091.13	8.2776651	8.4029516	8.4148206	-0.5666667	-0.4666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1252865	0.1371555	Branaplam-specific	-2.251402	SF3B3
ENSG00000026751.17	9.1854115	8.8787327	8.9119370	-0.3000000	-0.0666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3066789	-0.2734746	Branaplam-specific	-2.246607	SLAMF7
ENSG00000122359.18	7.6498416	6.2896423	7.5345641	-0.9666667	-0.9500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.3601993	-0.1152775	Branaplam-specific	-2.240435	ANXA11
ENSG00000113719.16	7.5501986	7.5005473	7.4881998	-0.8500000	0.1333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0496512	-0.0619988	Branaplam-specific	-2.233131	ERGIC1
ENSG00000138698.15	5.4944600	5.6202253	5.4513830	-0.4500000	-0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1257654	-0.0430770	Branaplam-specific	-2.220561	RAP1GDS1
ENSG00000189091.13	8.2776651	8.4029516	8.4148206	-0.5666667	-0.4666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1252865	0.1371555	Branaplam-specific	-2.209715	SF3B3
ENSG00000115840.14	5.5526802	4.9379561	5.5799193	-0.9666667	-0.1500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.6147242	0.0272391	Branaplam-specific	-2.208868	SLC25A12
ENSG00000167081.18	5.3475640	5.0713777	5.1798680	-0.9000000	-0.9166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2761862	-0.1676960	Branaplam-specific	-2.197212	PBX3
ENSG00000180104.16	6.1625641	5.4927133	6.2344432	-0.9500000	-0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.6698509	0.0718791	Branaplam-specific	-2.126322	EXOC3
ENSG00000134852.15	3.8881696	3.8964849	3.8645191	0.0000000	0.7166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0083154	-0.0236505	Branaplam-specific	-2.103294	CLOCK
ENSG00000117228.10	6.2113174	6.2289605	6.3039646	0.8000000	0.8833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0176431	0.0926473	Branaplam-specific	-2.094464	GBP1
ENSG00000176407.18	6.1227173	6.0800678	6.1379803	0.7166667	0.3666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0426495	0.0152631	Branaplam-specific	-2.092161	KCMF1
ENSG00000142634.13	7.3680775	7.5167513	7.6087441	-0.3333333	0.0500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1486738	0.2406666	Branaplam-specific	-2.086733	EFHD2
ENSG00000234127.9	7.2326711	7.3382892	7.3170587	1.0000000	0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1056181	0.0843876	Branaplam-specific	-2.073400	TRIM26
ENSG00000047621.12	4.8199364	4.5481914	4.6830428	-0.9166667	-0.7166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2717450	-0.1368936	Branaplam-specific	-2.068560	C12orf4
ENSG00000146757.14	4.2245115	4.2927393	3.9940874	0.7000000	0.0333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0682278	-0.2304240	Branaplam-specific	-2.056343	ZNF92
ENSG00000172469.16	5.5678175	5.2116111	5.3902509	-0.9500000	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3562064	-0.1775666	Branaplam-specific	-2.016101	MANEA
ENSG00000185920.16	4.0582967	4.2551289	4.3434077	0.3000000	0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1968322	0.2851109	Branaplam-specific	-2.013666	PTCH1
ENSG00000107290.14	7.5088671	7.1713742	7.3764320	-0.7500000	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3374929	-0.1324351	Risdiplam-specific	2.002415	SETX
ENSG00000123983.14	6.1040022	5.9942099	6.0578775	-0.8666667	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1097923	-0.0461247	Risdiplam-specific	2.015697	ACSL3
ENSG00000115415.20	10.4388782	9.7878886	9.3949206	-0.9333333	-0.9500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.6509896	-1.0439576	Risdiplam-specific	2.103504	STAT1
ENSG00000100485.12	4.5238499	4.4526611	3.8429537	-0.7833333	-0.8500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0711888	-0.6808962	Risdiplam-specific	2.140344	SOS2
ENSG00000160293.17	6.2055016	6.4723710	6.3220035	-0.2333333	-0.1500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2668694	0.1165019	Risdiplam-specific	2.252860	VAV2
ENSG00000256646.7	-Inf	-Inf	-Inf	-0.2738613	-0.2008316	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	NaN	Risdiplam-specific	2.261174	AC010132.3
ENSG00000106588.11	2.4132009	2.1824090	2.4939766	0.4333333	-0.0500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2307919	0.0807756	Risdiplam-specific	2.261174	PSMA2
ENSG00000119402.17	5.7926703	6.0848400	5.9770295	0.5666667	-0.2833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2921696	0.1843591	Risdiplam-specific	2.268566	FBXW2
ENSG00000112701.18	5.8132585	5.3349130	5.5127637	-0.9500000	-0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4783455	-0.3004948	Risdiplam-specific	2.295573	SENP6
ENSG00000069869.16	3.7094266	3.9353162	3.7883388	-0.3166667	0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2258896	0.0789122	Risdiplam-specific	2.300576	NEDD4
ENSG00000205268.11	5.8922730	5.9970607	6.0890504	-0.4833333	-0.0166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1047877	0.1967774	Risdiplam-specific	2.306077	PDE7A
ENSG00000164292.13	3.9204349	3.7821383	4.1821598	-0.8833333	0.8166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1382966	0.2617249	Risdiplam-specific	2.311566	RHOBTB3
ENSG00000107263.18	7.7481426	8.0216906	7.9613528	0.9333333	0.9666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2735480	0.2132102	Risdiplam-specific	2.345126	RAPGEF1
ENSG00000270800.3	-Inf	-6.1574410	-6.1170482	0.3729349	0.3168472	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	Inf	Inf	Risdiplam-specific	2.378209	RPS10-NUDT3
ENSG00000124614.16	0.0729407	0.6627380	1.0225031	0.9500000	0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.5897973	0.9495625	Risdiplam-specific	2.378209	RPS10
ENSG00000268790.5	-Inf	-Inf	-6.1170482	0.4107919	-0.4016632	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	Inf	Risdiplam-specific	2.396985	AC008764.4
ENSG00000214046.8	4.3300136	4.2001110	4.2547284	-0.8000000	-0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1299025	-0.0752851	Risdiplam-specific	2.396985	SMIM7
ENSG00000079616.13	6.7642928	6.9745767	6.8425915	-0.3166667	-0.5666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2102839	0.0782987	Risdiplam-specific	2.405511	KIF22
ENSG00000188822.8	4.6854929	4.5525044	4.6168145	-0.9833333	-0.1666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1329885	-0.0686784	Risdiplam-specific	2.471255	CNR2
ENSG00000158234.12	2.8341480	2.8924076	2.5729498	-0.2166667	-0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0582596	-0.2611982	Risdiplam-specific	2.506330	FAIM
ENSG00000071189.21	4.3992788	4.0857330	4.3351930	-0.9666667	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3135458	-0.0640858	Risdiplam-specific	2.546995	SNX13
ENSG00000092931.11	3.8965532	3.4124147	3.6724854	-0.9333333	-0.8500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.4841385	-0.2240678	Risdiplam-specific	2.582979	MFSD11
ENSG00000168310.11	6.6533029	6.5494867	6.4978916	-0.8833333	-0.7000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1038163	-0.1554113	Risdiplam-specific	2.602322	IRF2
ENSG00000082996.19	5.1709045	5.2782293	5.0628609	0.7500000	0.6000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1073248	-0.1080436	Risdiplam-specific	2.641557	RNF13
ENSG00000135974.10	4.1454717	3.9510835	3.9637693	-0.1500000	0.1166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1943882	-0.1817024	Risdiplam-specific	2.664718	C2orf49
ENSG00000056097.16	6.9803244	7.1103699	7.0268133	0.9000000	0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1300455	0.0464889	Risdiplam-specific	2.686858	ZFR
ENSG00000144228.9	4.6371177	4.5966114	4.5703275	0.1000000	-0.4666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0405063	-0.0667902	Risdiplam-specific	2.688732	SPOPL
ENSG00000197694.18	7.6158650	7.8129346	7.7234347	-0.6166667	-0.5833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1970696	0.1075697	Risdiplam-specific	2.736914	SPTAN1
ENSG00000164187.7	4.0948224	4.2034061	4.0641040	-0.6500000	-0.5833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1085837	-0.0307184	Risdiplam-specific	2.767962	LMBRD2
ENSG00000145725.19	5.7507703	5.5334301	5.6332400	-0.9833333	-0.7000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2173402	-0.1175302	Risdiplam-specific	2.820051	PPIP5K2
ENSG00000126457.21	8.9964156	8.8587580	8.5408842	-0.8166667	-1.0000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1376577	-0.4555314	Risdiplam-specific	2.855578	PRMT1
ENSG00000115942.9	4.9500416	4.9086482	4.8085062	-0.8666667	-0.8166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0413934	-0.1415354	Risdiplam-specific	2.872134	ORC2
ENSG00000108651.10	6.0570631	6.1625134	6.0820106	-0.5166667	-0.5000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1054503	0.0249475	Risdiplam-specific	2.881977	UTP6
ENSG00000116095.11	4.1874370	4.3690583	4.3165372	0.9333333	0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1816212	0.1291002	Risdiplam-specific	2.906637	PLEKHA3
ENSG00000135677.11	6.2738119	6.4291643	6.2158275	-0.1833333	-0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1553524	-0.0579844	Risdiplam-specific	2.925520	GNS
ENSG00000153310.19	6.6416164	6.4650685	6.4758759	-0.8000000	-0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1765479	-0.1657405	Risdiplam-specific	2.929163	CYRIB
ENSG00000123066.8	4.5321318	4.3865575	4.5013373	-0.9166667	-0.6000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1455743	-0.0307945	Risdiplam-specific	2.939934	MED13L
ENSG00000138413.13	6.0595426	5.9872173	5.4322551	-0.8333333	-0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0723253	-0.6272874	Risdiplam-specific	2.944458	IDH1
ENSG00000145050.19	7.8300980	7.4571539	7.7066176	-0.9833333	-0.8833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3729441	-0.1234804	Risdiplam-specific	2.945036	MANF
ENSG00000083799.17	7.1540124	7.5326662	7.3407174	0.3333333	-0.2666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.3786538	0.1867050	Risdiplam-specific	2.991397	CYLD
ENSG00000093000.19	7.1753150	7.1531718	7.2170854	-0.2333333	-0.6166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0221432	0.0417704	Risdiplam-specific	3.049978	NUP50
ENSG00000047365.12	4.3533805	4.0299111	4.5141288	-0.2333333	-0.2166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.3234694	0.1607483	Risdiplam-specific	3.070286	ARAP2
ENSG00000047056.16	4.0255494	4.0434576	4.1473944	-0.1000000	-0.0500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0179083	0.1218450	Risdiplam-specific	3.072126	WDR37
ENSG00000011376.12	6.1420513	6.0806652	6.1177692	-0.7833333	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0613861	-0.0242821	Risdiplam-specific	3.127228	LARS2
ENSG00000156469.9	4.4749894	4.2551289	3.9422962	-0.9000000	-0.9000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.2198605	-0.5326931	Risdiplam-specific	3.137840	MTERF3
ENSG00000112308.13	6.6352683	6.7454994	6.9682582	-0.3166667	0.9166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1102310	0.3329899	Risdiplam-specific	3.154727	C6orf62
ENSG00000105618.14	6.7530710	6.8565795	6.9014997	-0.4500000	-0.2500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1035086	0.1484288	Risdiplam-specific	3.184942	PRPF31
ENSG00000196116.8	5.4226531	5.3981068	5.3892594	0.5666667	0.0500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0245462	-0.0333937	Risdiplam-specific	3.242623	TDRD7
ENSG00000139626.16	8.4289367	8.5256085	8.7186075	-0.6833333	0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0966718	0.2896708	Risdiplam-specific	3.271285	ITGB7
ENSG00000103415.12	6.1555052	6.0952245	6.0569412	-0.8833333	-0.9000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0602808	-0.0985641	Risdiplam-specific	3.271732	HMOX2
ENSG00000150753.12	8.7913377	8.8172873	8.7974771	-0.5333333	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0259496	0.0061394	Risdiplam-specific	3.275364	CCT5
ENSG00000137878.17	-Inf	-Inf	-Inf	0.2738613	0.7137184	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	NaN	Risdiplam-specific	3.275735	GCOM1
ENSG00000255529.9	3.6339962	3.9019035	3.7393773	0.9166667	0.6500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2679073	0.1053811	Risdiplam-specific	3.275735	POLR2M
ENSG00000083720.13	6.8050233	6.7546999	6.7633006	-0.7666667	-0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0503234	-0.0417228	Risdiplam-specific	3.340651	OXCT1
ENSG00000133028.12	5.8801698	4.4636952	4.9901689	-0.9833333	-0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-1.4164747	-0.8900010	Risdiplam-specific	3.386642	SCO1
ENSG00000110075.14	6.7897693	6.7616086	6.7692199	-0.6666667	-0.7000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0281607	-0.0205493	Risdiplam-specific	3.407066	PPP6R3
ENSG00000188352.12	6.2083491	6.1574255	5.8454863	-0.8500000	-0.8000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0509237	-0.3628628	Risdiplam-specific	3.444138	FOCAD
ENSG00000130159.14	5.6697893	5.7517021	5.7067171	0.2666667	0.0833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0819128	0.0369277	Risdiplam-specific	3.486950	ECSIT
ENSG00000134779.15	6.4030684	6.4744182	6.2912815	-0.1500000	-0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0713497	-0.1117869	Risdiplam-specific	3.490282	TPGS2
ENSG00000136908.17	5.4260049	5.3142343	5.2907506	-0.9333333	-0.7166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1117706	-0.1352542	Risdiplam-specific	3.562029	DPM2
ENSG00000008083.14	4.9448917	5.3880062	5.1473944	-0.0833333	0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.4431145	0.2025027	Risdiplam-specific	3.661699	JARID2
ENSG00000102900.13	6.5508501	6.7217594	6.6187193	-0.3500000	-0.5833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1709092	0.0678692	Risdiplam-specific	3.739712	NUP93
ENSG00000235162.9	7.0215562	6.8476572	6.9780191	-0.9833333	-0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1738990	-0.0435371	Risdiplam-specific	3.754437	C12orf75
ENSG00000146007.11	6.4357612	6.4700929	6.4008672	0.1166667	-0.7166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0343318	-0.0348940	Risdiplam-specific	3.761796	ZMAT2
ENSG00000176142.13	4.9523113	4.8752936	5.0597483	-0.8000000	-0.4666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0770177	0.1074370	Risdiplam-specific	3.805878	TMEM39A
ENSG00000159063.13	5.2528677	5.1835218	4.7347008	-0.6666667	-0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0693459	-0.5181668	Risdiplam-specific	3.900791	ALG8
ENSG00000168297.16	4.4572719	4.5264309	4.3976658	0.2000000	0.7000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0691590	-0.0596060	Risdiplam-specific	3.991608	PXK
ENSG00000079332.15	5.9944819	5.9859423	5.9895147	-0.3333333	-0.7000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0085396	-0.0049672	Risdiplam-specific	4.011891	SAR1A
ENSG00000119414.11	6.3319944	6.1776702	6.1881585	-0.7833333	-0.9500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1543241	-0.1438358	Risdiplam-specific	4.112416	PPP6C
ENSG00000111252.11	6.0629114	6.0055797	6.3426395	-0.9333333	0.2333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0573317	0.2797282	Risdiplam-specific	4.151962	SH2B3
ENSG00000122643.22	6.6406786	6.5065618	6.6123601	0.6166667	0.6833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1341168	-0.0283185	Risdiplam-specific	4.343214	NT5C3A
ENSG00000283398.1	-4.7981191	-4.5724785	-5.1170482	0.3166667	0.2666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2256407	-0.3189291	Risdiplam-specific	4.608559	AC114737.4
ENSG00000173064.13	5.4954924	5.4998775	5.7980842	-0.6666667	0.5833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0043851	0.3025919	Risdiplam-specific	4.671793	HECTD4
ENSG00000177885.15	8.4372479	8.7097412	8.6053858	0.9000000	0.4666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2724933	0.1681379	Risdiplam-specific	4.821942	GRB2
ENSG00000112159.12	5.4312820	5.2391638	5.5182164	-0.8166667	-0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1921182	0.0869344	Risdiplam-specific	4.910025	MDN1
ENSG00000118596.12	3.7831582	3.8467795	3.7898424	-0.5833333	-0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0636214	0.0066842	Risdiplam-specific	4.924104	SLC16A7
ENSG00000149089.13	5.2158789	5.3263748	5.1213565	0.2833333	-0.8166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1104960	-0.0945223	Risdiplam-specific	5.036669	APIP
ENSG00000135272.11	6.8400399	6.8520378	6.9162027	-0.1000000	0.2333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0119979	0.0761628	Risdiplam-specific	5.123147	MDFIC
ENSG00000268746.1	-Inf	-Inf	-Inf	-0.0456435	0.2738613	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	NaN	NaN	Risdiplam-specific	5.171954	AC010519.1
ENSG00000063169.10	4.1399160	4.3233492	4.1473944	0.3833333	-0.2000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1834332	0.0074783	Risdiplam-specific	5.171954	BICRA
ENSG00000185019.17	3.5534098	3.6801870	3.6741147	-0.1166667	0.7333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1267772	0.1207049	Risdiplam-specific	5.180906	UBOX5
ENSG00000215251.4	5.7330058	5.6710923	5.5575854	0.1000000	-0.9000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0619135	-0.1754204	Risdiplam-specific	5.180906	FASTKD5
ENSG00000138182.14	5.4225883	5.3488666	5.1992333	-0.7000000	-0.8166667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0737216	-0.2233549	Risdiplam-specific	5.393297	KIF20B
ENSG00000184840.12	8.2545954	8.1966018	8.2168758	-0.9500000	-0.6500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0579936	-0.0377196	Risdiplam-specific	5.427913	TMED9
ENSG00000154001.14	6.1977946	6.3468815	6.2492740	0.7666667	0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.1490869	0.0514794	Risdiplam-specific	5.687174	PPP2R5E
ENSG00000132383.12	7.7774015	7.6521262	7.6758437	-0.9833333	-0.8500000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1252753	-0.1015578	Risdiplam-specific	6.285142	RPA1
ENSG00000102531.16	5.9941860	5.8126649	5.8716365	-0.9333333	-0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1815210	-0.1225495	Risdiplam-specific	6.386338	FNDC3A
ENSG00000033030.15	4.4037055	4.4378165	3.6692214	0.6833333	-0.9833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0341110	-0.7344841	Risdiplam-specific	6.732944	ZCCHC8
ENSG00000165806.21	4.8915779	4.7777241	4.7502305	-0.3333333	-0.8833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.1138538	-0.1413474	Risdiplam-specific	6.869295	CASP7
ENSG00000155324.10	3.4373384	3.6499140	3.7174228	-0.2666667	0.2666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.2125755	0.2800844	Risdiplam-specific	7.089980	GRAMD2B
ENSG00000162694.14	3.5415857	3.6140485	3.0850756	0.6000000	-0.8000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0724629	-0.4565101	Risdiplam-specific	7.608560	EXTL2
ENSG00000196422.11	2.3726765	2.4535838	2.6773676	0.5833333	0.3333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0809074	0.3046912	Risdiplam-specific	10.672749	PPP1R26
ENSG00000243147.8	4.6638297	4.7517021	4.5141288	0.2833333	-0.7833333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0878724	-0.1497009	Risdiplam-specific	10.674744	MRPL33
ENSG00000163697.17	4.8469728	4.9073018	4.9280288	-0.5500000	-0.6333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.0603290	0.0810560	Risdiplam-specific	12.729286	APBB2
ENSG00000154864.12	6.4592491	5.8319535	6.0927097	-0.9000000	-0.8000000	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.6272956	-0.3665394	Risdiplam-specific	15.785807	PIEZO2
ENSG00000070061.15	5.5878630	5.4909166	5.6378393	-0.7166667	-0.5333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-0.0969464	0.0499763	Risdiplam-specific	17.798155	ELP1
ENSG00000165475.15	3.9468619	0.7373768	3.5375878	-0.9833333	-0.9333333	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	-3.2094851	-0.4092741	Risdiplam-specific	21.628056	CRYL1
ENSG00000144036.16	2.7150069	3.1486207	2.7347008	0.9833333	0.6666667	Branaplam_100_LCL_polyA_1	Risdiplam_316_LCL_polyA_1	0.4336138	0.0196939	Risdiplam-specific	24.606656	EXOC6B

sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C           
 [4] LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C       
 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] forcats_0.5.1   stringr_1.4.0   dplyr_1.0.9     purrr_0.3.4    
[5] readr_2.1.2     tidyr_1.2.0     tibble_3.1.7    ggplot2_3.3.6  
[9] tidyverse_1.3.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     lubridate_1.8.0  assertthat_0.2.1 rprojroot_2.0.3 
 [5] digest_0.6.29    utf8_1.2.2       R6_2.5.1         cellranger_1.1.0
 [9] backports_1.4.1  reprex_2.0.1     evaluate_0.15    highr_0.9       
[13] httr_1.4.3       pillar_1.7.0     rlang_1.0.2      readxl_1.4.0    
[17] rstudioapi_0.13  whisker_0.4      jquerylib_0.1.4  rmarkdown_2.14  
[21] labeling_0.4.2   bit_4.0.4        munsell_0.5.0    broom_0.8.0     
[25] compiler_4.2.0   httpuv_1.6.5     modelr_0.1.8     xfun_0.30       
[29] pkgconfig_2.0.3  htmltools_0.5.2  tidyselect_1.1.2 workflowr_1.7.0 
[33] fansi_1.0.3      crayon_1.5.1     tzdb_0.3.0       dbplyr_2.1.1    
[37] withr_2.5.0      later_1.3.0      grid_4.2.0       jsonlite_1.8.0  
[41] gtable_0.3.0     lifecycle_1.0.1  DBI_1.1.2        git2r_0.30.1    
[45] magrittr_2.0.3   scales_1.2.0     vroom_1.5.7      cli_3.3.0       
[49] stringi_1.7.6    farver_2.1.0     fs_1.5.2         promises_1.2.0.1
[53] xml2_1.3.3       bslib_0.3.1      ellipsis_0.3.2   generics_0.1.2  
[57] vctrs_0.4.1      tools_4.2.0      bit64_4.0.5      glue_1.6.2      
[61] hms_1.1.1        parallel_4.2.0   fastmap_1.1.0    yaml_2.3.5      
[65] colorspace_2.0-3 rvest_1.0.2      knitr_1.39       haven_2.5.0     
[69] sass_0.4.1

Check introns with unique specificities

2023-03-06

Recheck list of risdi/brana-specific introns