Tables summarising the TWAS results

Table showing the significant transcripts

Count the numbers of significant genes

Last updated: 2021-03-05

Checks: 7 0

Knit directory: fitnessGWAS/

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library(tidyverse)
library(DT)
library(kableExtra)

kable_table <- function(df) { # cool tables
  kable(df, "html") %>%
  kable_styling() %>%
  scroll_box(height = "300px")
}

my_data_table <- function(df){ # Make html tables:
  datatable(
    df, rownames=FALSE,
    autoHideNavigation = TRUE,
    extensions = c("Scroller",  "Buttons"),
    options = list(
      dom = 'Bfrtip',
      deferRender=TRUE,
      scrollX=TRUE, scrollY=400,
      scrollCollapse=TRUE,
      buttons = 
        list('pageLength', 'colvis', 'csv', list(
          extend = 'pdf',
          pageSize = 'A4',
          orientation = 'landscape',
          filename = 'TWAS_sig_genes')),
      pageLength = 50
    )
  )
}

sig_transcripts_table <- read_csv("data/derived/TWAS/sig_transcripts_table.csv")

tallies <- sort(table(sig_transcripts_table$type))

big_table <- sig_transcripts_table %>%
  select(-type) %>%
  left_join(
    sig_transcripts_table %>%
      group_by(FBID) %>%
      summarise(type = list(type), .groups = "drop") %>%
      mutate(type = str_remove_all(map_chr(type, ~ paste0(.x, collapse = "; ")), "sig_")),
    by = "FBID") %>%
  select(FBID, gene_name, type, chromosome, AveExpr, male_bias_in_expression, everything()) %>%
  mutate(chromosome = replace(chromosome, is.na(chromosome), "Unknown")) %>%
  select(-gene_symbol, -entrez_id) %>%
  arrange(-P_sex_antag) %>%
  rename(`Gene name` = gene_name,
         Significance = type,
         Chromosome = chromosome,
         `Female early` = beta_FE,
         `Female late` = beta_FL,
         `Male early` = beta_ME,
         `Male late` = beta_ML,
         `Male bias in expression (logFC)` = male_bias_in_expression,
         `Average expression level` = AveExpr) %>%
  rename_all(~ str_remove_all(.x, "ED[_]")) %>%
  distinct()

Table showing the significant transcripts

The table shows the 784 transcripts that were significant in one or more ways (shown in the ‘significance’ column), e.g. transcripts whose abundance showed a sexually antagonistic relationship with fitness in the early-life assays are denoted SA_early. Columns 7-10 show the mashr-adjusted regression coefficients that relate the line mean transcript abundance to the line mean fitnesses. The last five columns give the mixture assignment probabilities from mashr. Abbreviations: AC = age concordant, SC = sexually concordant, SA = sexually antagonistic.

We define significantly antagonistic transcripts as those where the relationship with fitness is significantly positive for one sex (or age class) and significantly negative for the other, with LFSR < 0.05. Similarly, we define significantly concordant transcripts as those where the relationship with fitness is significantly positive for one sex or age class and also significantly positive for the other (LFSR < 0.05). This is quite conservative, because a transcript needs to have a LFSR < 0.05 for two tests, giving two chances for a ‘false negative’.

big_table %>%  my_data_table()

Search:

FBID	Gene name	Significance	Chromosome	Average expression level	Male bias in expression (logFC)	Female early	Female late	Male early	Male late	LFSR_FE	LFSR_FL	LFSR_ME	LFSR_ML	P_equal_effects	P_female_specific	P_male_specific	P_null	P_sex_antag	female_narrow_heritability	male_narrow_heritability

FBID	Gene name	Significance	Chromosome	Average expression level	Male bias in expression (logFC)	Female early	Female late	Male early	Male late	LFSR_FE	LFSR_FL	LFSR_ME	LFSR_ML	P_equal_effects	P_female_specific	P_male_specific	P_null	P_sex_antag	female_narrow_heritability	male_narrow_heritability
FBgn0013275	Heat-shock-protein-70Aa	SA_early; SA_late; AC_females; AC_males	3R	4.99	-0.01	-0.11	-0.11	0.11	0.11	0	0.01	0	0	0	0.01	0.01	0	0.98	0	0
FBgn0259845	ncRNA	SA_early; SA_late; AC_females; AC_males	Y	6.21	0	-0.2	-0.19	0.24	0.24	0	0	0	0	0	0	0.02	0	0.98	0.08	0.07
XLOC_001400		SA_early; SA_late; AC_females; AC_males	Unknown	5.49	0.44	-0.16	-0.15	0.11	0.11	0	0	0	0	0	0.02	0	0	0.98	0	0.01
FBgn0027330	lethal (1) G0020	SA_early; SA_late; AC_females; AC_males	X	5.92	-0.73	-0.36	-0.35	0.34	0.34	0.01	0.01	0.02	0.02	0	0.02	0.01	0	0.96	0.15	0
FBgn0263092	pseudo	SA_early; SA_late; AC_females; AC_males	2R	5.2	-0.06	-0.24	-0.24	0.25	0.25	0.01	0.01	0	0	0	0.01	0.03	0	0.96	0.01	0.01
XLOC_006200		SA_early; SA_late; AC_females; AC_males	Unknown	5.49	0.25	-0.19	-0.19	0.14	0.14	0	0	0.01	0.01	0	0.04	0.01	0	0.96	0	0.06
FBgn0000022	achaete	SA_early; SA_late; AC_females; AC_males	X	5.29	-0.13	-0.3	-0.3	0.21	0.21	0	0	0.02	0.02	0	0.05	0	0	0.95	0.06	0.13
FBgn0037389	pseudo	SA_early; SA_late; AC_females; AC_males	3R	5.87	0.42	0.09	0.09	-0.07	-0.07	0.01	0.01	0.02	0.02	0	0.03	0.01	0	0.95	0.01	0.06
FBgn0085658		SA_early; SA_late; AC_females; AC_males	Unknown	5.64	0.61	0.07	0.07	-0.05	-0.05	0.01	0.01	0.02	0.02	0	0.04	0.01	0.01	0.95	0.05	0.12
FBgn0261615	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	X	5.92	-1.7	0.14	0.14	-0.19	-0.19	0.01	0.01	0	0	0	0.01	0.04	0	0.95	0.64	0
XLOC_001062		SA_early; SA_late; AC_females; AC_males	Unknown	5.23	0.25	-0.2	-0.19	0.22	0.22	0.01	0.01	0.01	0	0	0.01	0.04	0	0.95	0	0
FBgn0038859	Odorant-binding protein 93a	SA_early; SA_late; AC_females; AC_males	3R	5.44	-0.07	-0.08	-0.08	0.1	0.1	0.03	0.03	0.01	0.01	0	0.01	0.05	0	0.94	0.01	0.18
FBgn0040733	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	2R	6.61	0.13	0.08	0.08	-0.11	-0.11	0.02	0.02	0.01	0.01	0	0.01	0.05	0	0.94	0.36	0.28
FBgn0261708		SA_early; SA_late; AC_females; AC_males	Unknown	5.45	0.21	0.08	0.07	-0.07	-0.07	0.03	0.03	0.03	0.03	0	0.03	0.02	0.01	0.94	0.01	0.1
FBgn0004782	Ccp84Ab	SA_early; SA_late; AC_females; AC_males	3R	5.66	0.1	-0.26	-0.26	0.19	0.19	0.01	0.01	0.02	0.02	0	0.04	0.02	0	0.93	0.06	0.02
FBgn0265254	long non-coding RNA:CR44268	SA_early; SA_late; AC_females; AC_males	2L	6.07	-0.06	-0.07	-0.07	0.06	0.06	0.03	0.04	0.04	0.04	0	0.04	0.02	0.02	0.92	0.22	0.15
XLOC_003546		SA_early; SA_late; AC_females; AC_males	Unknown	4.98	-0.02	-0.15	-0.15	0.12	0.12	0.02	0.03	0.02	0.02	0	0.04	0.03	0.01	0.92	0.57	0.6
XLOC_004306		SA_early; SA_late; AC_females; AC_males	Unknown	5.19	0.04	-0.14	-0.14	0.13	0.13	0.03	0.03	0.02	0.02	0	0.03	0.04	0.01	0.92	0	0
XLOC_004454		SA_early; SA_late; AC_females; AC_males	Unknown	5.32	0.03	-0.19	-0.19	0.24	0.24	0.02	0.02	0.01	0.01	0	0.01	0.06	0	0.92	0	0
FBgn0037832	Desiccate	SA_early; SA_late; AC_females; AC_males	3R	5.46	0.23	-0.24	-0.23	0.19	0.19	0.01	0.01	0.03	0.03	0	0.07	0.01	0	0.91	0.29	0.15
FBgn0051327	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	3R	5.79	1.23	-0.27	-0.26	0.2	0.2	0.03	0.03	0.02	0.02	0	0.03	0.04	0.01	0.91	0.11	0.67
FBgn0085365		SA_early; SA_late; AC_females; AC_males	Unknown	5.45	-0.15	0.09	0.09	-0.09	-0.09	0.03	0.03	0.05	0.05	0.01	0.04	0.03	0.01	0.91	0.12	0.07
FBgn0086030	ncRNA	SA_early; AC_males	2R	5.28	0	0.07	0.07	-0.1	-0.1	0.05	0.05	0.02	0.02	0	0.01	0.07	0.01	0.91	0.02	0.08
FBgn0003931	small nuclear RNA U4 at 38AB	AC_males	2L	5.98	-0.12	-0.05	-0.05	0.07	0.07	0.06	0.07	0.03	0.03	0	0.01	0.06	0.01	0.91	0.27	0.09
FBgn0265349	Seminal fluid protein 33A4	SA_early; SA_late; AC_females; AC_males	2L	6.18	0.78	0.13	0.13	-0.08	-0.08	0	0	0.04	0.04	0	0.1	0	0	0.9	0.06	0.54
FBgn0036110	Cuticular protein 67Fb	AC_males	3L	5.24	0.28	-0.07	-0.06	0.09	0.09	0.09	0.1	0.01	0.01	0.01	0.01	0.08	0.01	0.9	0	0.25
FBgn0262404	mir-996 stem loop	AC_males	3R	5.75	-0.08	0.06	0.06	-0.08	-0.08	0.06	0.07	0.03	0.03	0.01	0.02	0.06	0.02	0.9	0.04	0.1
XLOC_002307		AC_males	Unknown	5.07	0	-0.07	-0.07	0.06	0.06	0.05	0.05	0.05	0.05	0.01	0.04	0.03	0.02	0.9	0.05	0.1
FBgn0016698	Phosphotyrosyl phosphatase activator	SA_early; SA_late; AC_females; AC_males	2L	6.37	-0.07	0.17	0.17	-0.15	-0.15	0.03	0.04	0.04	0.04	0.01	0.05	0.04	0.01	0.89	0.1	0.18
FBgn0034099	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	2R	5.82	0.82	-0.26	-0.25	0.16	0.16	0	0.01	0.03	0.03	0	0.1	0.01	0	0.89	0.01	0.14
FBgn0040531	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	3R	5.07	-0.01	-0.21	-0.21	0.15	0.15	0.01	0.01	0.04	0.04	0	0.09	0.02	0.01	0.89	0	0
FBgn0263029	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	2R	5.97	0.36	-0.13	-0.13	0.1	0.1	0.02	0.02	0.05	0.05	0	0.08	0.01	0.01	0.89	0	0.14
FBgn0264701	long non-coding RNA:CR43970	SA_early; SA_late; AC_females; AC_males	3L	5.17	0.03	0.19	0.18	-0.12	-0.12	0.01	0.01	0.04	0.03	0	0.09	0.01	0	0.89	0	0.1
XLOC_004689		SA_early; SA_late; AC_females; AC_males	Unknown	5	-0.01	-0.2	-0.19	0.28	0.28	0.03	0.03	0.01	0.01	0	0.01	0.1	0	0.89	0.03	0.09
XLOC_000820		AC_males	Unknown	5.33	0.17	-0.12	-0.12	0.11	0.11	0.05	0.06	0.03	0.03	0.01	0.03	0.05	0.01	0.89	0.26	0.29
FBgn0014019	Rhodopsin 5	SA_early; AC_males	2L	6.16	0.33	-0.16	-0.16	0.17	0.16	0.05	0.05	0.02	0.02	0.01	0.03	0.08	0.01	0.88	0.44	0.34
FBgn0020645	Lcp65Aa	SA_early; SA_late; AC_females; AC_males	3L	5.29	0.4	-0.3	-0.29	0.16	0.16	0	0	0.03	0.03	0	0.12	0	0	0.88	0.07	0.02
FBgn0033054	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	2R	5.98	0.45	-0.27	-0.26	0.19	0.19	0.02	0.02	0.05	0.05	0.01	0.08	0.02	0.01	0.88	0.1	0.15
FBgn0034474	Odorant-binding protein 56g	SA_early; SA_late; AC_females; AC_males	2R	6.44	1.17	-0.11	-0.1	0.21	0.21	0.02	0.02	0.02	0.02	0	0.01	0.1	0	0.88	0.11	0.51
FBgn0036793	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	3L	5.48	0.47	-0.19	-0.19	0.15	0.15	0.04	0.04	0.04	0.04	0.01	0.06	0.04	0.01	0.88	0.18	0.2
FBgn0050269	uncharacterized protein	SA_early; SA_late; AC_females; AC_males	2R	6.35	0.16	0.13	0.13	-0.14	-0.14	0.03	0.04	0.05	0.05	0.01	0.05	0.05	0.01	0.88	0.22	0.23
FBgn0053109	uncharacterized protein	SA_early; AC_males	3R	6.24	-0.06	0.06	0.05	-0.12	-0.12	0.05	0.06	0	0	0	0	0.12	0	0.88	0.74	0.79
FBgn0039846	Polynucleotide phosphorylase	AC_females	3R	5.79	-0.39	-0.34	-0.33	0.21	0.21	0.01	0.01	0.06	0.05	0	0.11	0.01	0	0.88	0.19	0
FBgn0050151	uncharacterized protein	AC_females	2R	6.13	0.32	0.11	0.11	-0.11	-0.11	0.04	0.04	0.06	0.05	0.01	0.05	0.04	0.02	0.88	0.07	0.07
FBgn0036670	uncharacterized protein	SA_early; AC_males	3L	5.56	0.71	0.15	0.15	-0.14	-0.14	0.05	0.05	0.05	0.05	0.01	0.05	0.06	0.01	0.87	0.12	0.1
FBgn0040729	uncharacterized protein	AC_females	2R	6.43	-0.03	0.07	0.07	-0.04	-0.04	0.04	0.04	0.09	0.09	0.01	0.09	0.01	0.02	0.87	0.13	0.14
FBgn0040099	lectin-28C	AC_males	2L	5.65	0.24	0.05	0.05	-0.07	-0.07	0.11	0.12	0.05	0.05	0.01	0.02	0.07	0.03	0.87	0.66	0.65
XLOC_004857		SA_early; SA_late; AC_females; AC_males	Unknown	5.7	-0.02	-0.2	-0.19	0.35	0.35	0.03	0.04	0	0	0	0	0.13	0	0.86	0	0.03
FBgn0028949	uncharacterized protein	AC_females	2L	5.36	0.25	0.14	0.14	-0.11	-0.11	0.04	0.04	0.07	0.07	0.01	0.08	0.03	0.02	0.86	0.4	0.27
FBgn0085736	uncharacterized protein	AC_females	3L	5.33	-0.03	-0.1	-0.1	0.05	0.05	0.01	0.01	0.08	0.08	0	0.13	0	0.01	0.86	0.05	0.01

Showing 1 to 50 of 784 entries

Previous1 2 3 4 5…16Next

Count the numbers of significant genes

Abbreviations: AC = age concordant, SC = sexually concordant, SA = sexually antagonistic.

tallies %>%
  enframe() %>%
  arrange(-value) %>%
  mutate(x = str_remove_all(name, "sig_"),
         `Number statistically significant` = value) %>%
  mutate(x = str_replace_all(x, "AC", "Age concordant"),
         x = str_replace_all(x, "SC", "Sexually concordant"),
         x = str_replace_all(x, "SA", "Sexually angatonistic"),
         x = str_replace_all(x, "_females", " (in females)"),
         x = str_replace_all(x, "_males", " (in males)"),
         x = str_replace_all(x, "_early", " (in early life)"),
         x = str_replace_all(x, "_late", " (in late life)")) %>%
  rename(`Type of transcript` = x) %>%
  select(`Type of transcript`, `Number statistically significant`) %>%
  kable_table()

Type of transcript	Number statistically significant
Age concordant (in males)	483
Age concordant (in females)	466
Sexually concordant (in late life)	142
Sexually concordant (in early life)	132
Sexually angatonistic (in early life)	40
Sexually angatonistic (in late life)	35

sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] kableExtra_1.1.0 DT_0.13          forcats_0.5.0    stringr_1.4.0   
 [5] dplyr_1.0.0      purrr_0.3.4      readr_1.3.1      tidyr_1.1.0     
 [9] tibble_3.0.1     ggplot2_3.3.2    tidyverse_1.3.0  workflowr_1.6.2 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6      lubridate_1.7.8   lattice_0.20-41   assertthat_0.2.1 
 [5] rprojroot_1.3-2   digest_0.6.25     R6_2.4.1          cellranger_1.1.0 
 [9] backports_1.1.7   reprex_0.3.0      evaluate_0.14     highr_0.8        
[13] httr_1.4.1        pillar_1.4.4      rlang_0.4.6       readxl_1.3.1     
[17] rstudioapi_0.11   whisker_0.4       blob_1.2.1        rmarkdown_2.5    
[21] webshot_0.5.2     htmlwidgets_1.5.1 munsell_0.5.0     broom_0.5.6      
[25] compiler_4.0.3    httpuv_1.5.3.1    modelr_0.1.8      xfun_0.19        
[29] pkgconfig_2.0.3   htmltools_0.5.0   tidyselect_1.1.0  fansi_0.4.1      
[33] viridisLite_0.3.0 crayon_1.3.4      dbplyr_1.4.4      withr_2.2.0      
[37] later_1.0.0       grid_4.0.3        nlme_3.1-149      jsonlite_1.7.0   
[41] gtable_0.3.0      lifecycle_0.2.0   DBI_1.1.0         git2r_0.27.1     
[45] magrittr_2.0.1    scales_1.1.1      cli_2.0.2         stringi_1.5.3    
[49] fs_1.4.1          promises_1.1.0    xml2_1.3.2        ellipsis_0.3.1   
[53] generics_0.0.2    vctrs_0.3.0       tools_4.0.3       glue_1.4.2       
[57] hms_0.5.3         crosstalk_1.1.0.1 yaml_2.2.1        colorspace_1.4-1 
[61] rvest_0.3.5       knitr_1.30        haven_2.3.1