Analysis of pulse-seq data from Montoro et al.

Introduction and Code

I fit 30 factors with normal-mixture priors to the pulse-seq dataset discussed in Montoro et al. I removed all genes with zero total counts and did a log1p transform of the counts. I used the following calls.

# Add 30 factors with rough backfits after every 5 factors.
fl <- flashier(data, greedy.Kmax = 30, var.type = 1, prior.type = "normal.mix", ash.param = list(optmethod = "mixSQP"), backfit.every = 5, final.backfit = TRUE, backfit.order = "montaigne", warmstart.backfits = FALSE)
# Process time on RCC cluster: 92 minutes

# Do a more thorough backfit.
fl <- flashier(data, flash.init = fl, greedy.Kmax = 0, var.type = 1, prior.type = "normal.mix", ash.param = list(optmethod = "mixSQP"), final.backfit = TRUE, backfit.order = "dropout", warmstart.backfits = FALSE, backfit.maxiter = 500)
# Process time: 266 minutes

The following code is used to produce the boxplots and tables below.

suppressMessages({
  library(ggplot2)
  library(topGO)
  library(org.Mm.eg.db)
})
#> Warning: package 'ggplot2' was built under R version 3.4.4

fl <- readRDS("~/Downloads/PulseSeq30_backfit.rds")
# Remove large data object to free up memory.
fl$fit$Y <- NULL

# Data frame containing cell type and loadings for each factor.
PSdf <- data.frame(fl$loadings$normalized.loadings[[2]])
cell.names <- rownames(fl$loadings$normalized.loadings[[2]])
cell.types <- as.factor(sapply(strsplit(cell.names, "_"), `[`, 5))
levels(cell.types) <- c("Bas", "Cil", "Clb", "Hil", "Gb1", "Gb2", "GbP",
                        "Ion", "Nec", "Prl", "Tf1", "Tf2", "TfP")
PSdf$cell.type <- cell.types

# Need to select signficant genes for topGO.
#   Scale gene loadings by scale constant * maximum cell loading.
s <- fl$loadings$scale.constant * 
  apply(abs(fl$loadings$normalized.loadings[[2]]), 2, max)
gene.loadings <- fl$loadings$normalized.loadings[[1]]
gene.loadings <- gene.loadings * rep(s, each = nrow(gene.loadings))
#   Get a pseudo-t statistic by dividing by the residual SE.
gene.t <- gene.loadings * sqrt(fl$fit$tau)
#   Convert to a p-value.
gene.p <- 2 * (1 - pnorm(abs(gene.t)))
#   Select significant genes using Benjamini-Hochberg.
BH <- function(k, alpha = 0.01) {
  pvals <- gene.p[, k]
  selected <- rep(0, length(pvals))
  names(selected) <- names(pvals)
  
  n <- length(pvals)
  sorted.pvals <- sort(pvals)
  BH <- sorted.pvals < alpha / (n - 0:(n - 1))
  cutoff <- min(which(!BH))
  selected[pvals < sorted.pvals[cutoff]] <- 1
  
  return(selected)
}
gene.sig <- sapply(1:ncol(gene.p), BH)

# How many significant genes per factor are there?
colSums(gene.sig)
#>  [1]  319  565   42   79  192    2  171  194   36 1495    1 1946    0   72
#> [15]   11   54    0   84    0  246  135    0  210   19    0  112  180  159
#> [29]  188  929

# I will only look at the factors with at least ten significant genes.
kset <- (1:ncol(gene.p))[colSums(gene.sig) > 9]

# I also want to see which factors contain genes mentioned in the paper.
paper.genes <- data.frame(
  gene = c("Nfia", "Ascl1", "Ascl2", "Ascl3", "Foxq1", "Cdhr3", "Rgs13",
           "Muc5b", "Notch2", "Il13ra1", "Krt4", "Krt13", "Krt8", "Ecm1",
           "S100a11", "Cldn3", "Lgals3", "Anxa1", "Il25", "Tslp", "Alox5ap",
           "Ptprc", "Pou2f3", "Gfi1b", "Spib", "Sox9", "Gp2", "Tff1",
           "Tff2", "Lman1l", "P2rx4", "Muc5ac", "Dcpp1", "Dcpp2", "Dcpp3",
           "Atp6v1c2", "Atp6v0d2", "Cftr"),
  type = c("Club", "NEC", "Tuft", "Ion", "Goblet", "Cil", "Tuft",
           "Club", "Club", "Club", "Hill", "Hill", "Basal", "Hill",
           "Hill", "Hill", "Hill", "Hill", "Tuft", "Tuft", "Tuft2",
           "Tuft2", "Tuft1", "Tuft2", "Tuft2", "Tuft2", "Goblet", "Gob1",
           "Gob1", "Gob1", "Gob1", "Gob1", "Gob2", "Gob2", "Gob2",
           "Ion", "Ion", "Ion"))
paper.genes$gene <- as.character(paper.genes$gene)
levels(paper.genes$type) <- c("Basal", "Ciliated", "Club", "Goblet-1",
                              "Goblet-2", "Goblet", "Hillock", "Ionocyte",
                              "Neuroendocrine", "Tuft", "Tuft-1", "Tuft-2")

# Set up topGOdata object.
GO.list <- as.factor(gene.sig[, 1])
GOdata <- new("topGOdata", ontology = "BP", allGenes = GO.list,
              annot = annFUN.org, mapping = "org.Mm.eg", ID = "symbol")
#> 
#> Building most specific GOs .....
#>  ( 11574 GO terms found. )
#> 
#> Build GO DAG topology ..........
#>  ( 15465 GO terms and 36320 relations. )
#> 
#> Annotating nodes ...............
#>  ( 17307 genes annotated to the GO terms. )

# Loop over kset.
for (k in kset) {
  cat(paste("## Factor", k, "\n"))
  fctr <- paste0("X", k)
  plot(ggplot(PSdf, aes_string(x = "cell.type", y = fctr)) +
         geom_boxplot(outlier.shape = NA, color = "red") +
         geom_jitter(position = position_jitter(0.2), cex = 0.1) +
         labs(x = "Cell Type", y = paste("Factor", k, "value")))
  
  mentions <- which(gene.sig[paper.genes$gene, k] == 1)
  if (length(mentions) > 0) {
    mentions.df <- paper.genes[mentions, ]
    mentions.df$t.val <- gene.t[names(mentions), k]
    cat("Significant genes that are also mentioned in the paper:\n")
    print(knitr::kable(mentions.df))
    cat("\n")
  }
  
  cat("Gene Ontology terms:\n")
  GOdata@allScores <- as.factor(gene.sig[, k])
  result <- suppressMessages(
    runTest(GOdata, algorithm = "classic", statistic = "fisher")
  )
  allRes <- GenTable(GOdata, classic = result, topNodes = 10)
  print(knitr::kable(allRes))
  cat("\n")
}

Factor 1

Expand here to see past versions of factors2-1.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
13	Krt8	Basal	-10.188834
15	S100a11	Hillock	-19.542238
16	Cldn3	Hillock	-5.084911
17	Lgals3	Hillock	-11.369577
18	Anxa1	Hillock	-12.864415

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0006412	translation	554	84	9.51	< 1e-30
GO:0043043	peptide biosynthetic process	575	84	9.87	< 1e-30
GO:0006518	peptide metabolic process	700	90	12.01	< 1e-30
GO:0043604	amide biosynthetic process	644	85	11.05	< 1e-30
GO:0043603	cellular amide metabolic process	830	91	14.24	< 1e-30
GO:1901566	organonitrogen compound biosynthetic pro…	1460	106	25.05	< 1e-30
GO:0034641	cellular nitrogen compound metabolic pro…	5337	177	91.59	5.7e-25
GO:0044271	cellular nitrogen compound biosynthetic …	3940	148	67.61	8.2e-25
GO:0044249	cellular biosynthetic process	4799	162	82.35	1.0e-22
GO:1901576	organic substance biosynthetic process	4895	163	84.00	3.1e-22

Factor 2

Expand here to see past versions of factors2-2.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
6	Cdhr3	Ciliated	23.243771
16	Cldn3	Hillock	5.531131

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0044782	cilium organization	291	89	8.61	<1e-30
GO:0060271	cilium assembly	272	82	8.05	<1e-30
GO:0003341	cilium movement	69	45	2.04	<1e-30
GO:0007018	microtubule-based movement	242	70	7.16	<1e-30
GO:0070925	organelle assembly	672	104	19.88	<1e-30
GO:0030031	cell projection assembly	450	85	13.31	<1e-30
GO:0120031	plasma membrane bounded cell projection …	443	84	13.11	<1e-30
GO:0007017	microtubule-based process	639	99	18.90	<1e-30
GO:0035082	axoneme assembly	60	37	1.78	<1e-30
GO:0001578	microtubule bundle formation	88	39	2.60	<1e-30

Factor 3

Expand here to see past versions of factors2-3.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
8	Muc5b	Club	-6.440982

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0006412	translation	554	17	1.31	2.3e-15
GO:0043043	peptide biosynthetic process	575	17	1.36	4.2e-15
GO:0043604	amide biosynthetic process	644	17	1.53	2.7e-14
GO:0006518	peptide metabolic process	700	17	1.66	1.0e-13
GO:0043603	cellular amide metabolic process	830	17	1.97	1.6e-12
GO:0042274	ribosomal small subunit biogenesis	68	7	0.16	2.1e-10
GO:0022613	ribonucleoprotein complex biogenesis	379	11	0.90	8.4e-10
GO:0019730	antimicrobial humoral response	51	6	0.12	2.0e-09
GO:0042254	ribosome biogenesis	251	9	0.59	5.7e-09
GO:1901566	organonitrogen compound biosynthetic pro…	1460	17	3.46	1.1e-08

Factor 4

Expand here to see past versions of factors2-4.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
14	Ecm1	Hillock	5.592506

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0006412	translation	554	36	2.24	< 1e-30
GO:0043043	peptide biosynthetic process	575	36	2.33	< 1e-30
GO:0006518	peptide metabolic process	700	37	2.83	< 1e-30
GO:0043604	amide biosynthetic process	644	36	2.60	< 1e-30
GO:0043603	cellular amide metabolic process	830	37	3.36	1.6e-30
GO:1901566	organonitrogen compound biosynthetic pro…	1460	37	5.91	7.7e-22
GO:0009059	macromolecule biosynthetic process	4091	49	16.55	2.6e-16
GO:0044271	cellular nitrogen compound biosynthetic …	3940	48	15.94	4.0e-16
GO:0034645	cellular macromolecule biosynthetic proc…	3989	48	16.13	6.7e-16
GO:0010467	gene expression	4479	50	18.12	1.8e-15

Factor 5

Expand here to see past versions of factors2-5.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
2	Ascl1	Neuroendocrine	-10.429897
7	Rgs13	Tuft	-49.037686
15	S100a11	Hillock	6.507033
17	Lgals3	Hillock	6.300152
19	Il25	Tuft	-12.456328
21	Alox5ap	Tuft-2	-10.525482
23	Pou2f3	Tuft-1	-7.369498
25	Spib	Tuft-2	-17.079978
26	Sox9	Tuft-2	-7.225993

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0006518	peptide metabolic process	700	27	6.92	1.2e-09
GO:0043603	cellular amide metabolic process	830	29	8.20	2.7e-09
GO:0043604	amide biosynthetic process	644	22	6.36	4.0e-07
GO:0006412	translation	554	20	5.47	6.0e-07
GO:0043043	peptide biosynthetic process	575	20	5.68	1.1e-06
GO:0050896	response to stimulus	6576	94	64.97	4.5e-06
GO:0050909	sensory perception of taste	51	6	0.50	1.1e-05
GO:0007186	G-protein coupled receptor signaling pat…	685	20	6.77	1.5e-05
GO:0006575	cellular modified amino acid metabolic p…	146	9	1.44	1.5e-05
GO:0050900	leukocyte migration	276	12	2.73	2.0e-05

Factor 7

Expand here to see past versions of factors2-6.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
2	Ascl1	Neuroendocrine	44.60350
7	Rgs13	Tuft	-13.99407

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0007610	behavior	617	25	5.70	4.8e-10
GO:0099504	synaptic vesicle cycle	119	11	1.10	1.3e-08
GO:0048489	synaptic vesicle transport	127	11	1.17	2.6e-08
GO:0097480	establishment of synaptic vesicle locali…	127	11	1.17	2.6e-08
GO:0099003	vesicle-mediated transport in synapse	128	11	1.18	2.9e-08
GO:0097479	synaptic vesicle localization	134	11	1.24	4.6e-08
GO:0003008	system process	1429	35	13.21	7.5e-08
GO:0033555	multicellular organismal response to str…	84	9	0.78	8.0e-08
GO:0006887	exocytosis	295	15	2.73	1.0e-07
GO:0050877	nervous system process	867	26	8.02	1.0e-07

Factor 8

Expand here to see past versions of factors2-7.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
15	S100a11	Hillock	-6.882840
17	Lgals3	Hillock	-8.554270
18	Anxa1	Hillock	-6.871433

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0007049	cell cycle	1476	110	15.27	<1e-30
GO:0051301	cell division	526	75	5.44	<1e-30
GO:0022402	cell cycle process	947	89	9.79	<1e-30
GO:0000278	mitotic cell cycle	733	79	7.58	<1e-30
GO:1903047	mitotic cell cycle process	567	71	5.86	<1e-30
GO:0007059	chromosome segregation	285	56	2.95	<1e-30
GO:0000280	nuclear division	362	49	3.74	<1e-30
GO:0098813	nuclear chromosome segregation	222	40	2.30	<1e-30
GO:0048285	organelle fission	410	49	4.24	<1e-30
GO:0140014	mitotic nuclear division	231	40	2.39	<1e-30

Factor 9

Expand here to see past versions of factors2-8.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0009059	macromolecule biosynthetic process	4091	21	6.62	1.3e-08
GO:0034645	cellular macromolecule biosynthetic proc…	3989	20	6.45	7.5e-08
GO:0035914	skeletal muscle cell differentiation	69	5	0.11	8.0e-08
GO:0006412	translation	554	9	0.90	1.3e-07
GO:0071310	cellular response to organic substance	1800	14	2.91	1.6e-07
GO:0043043	peptide biosynthetic process	575	9	0.93	1.8e-07
GO:0031324	negative regulation of cellular metaboli…	2194	15	3.55	2.5e-07
GO:0044249	cellular biosynthetic process	4799	21	7.76	2.7e-07
GO:0070887	cellular response to chemical stimulus	2239	15	3.62	3.2e-07
GO:1901576	organic substance biosynthetic process	4895	21	7.92	3.9e-07

Factor 10

Expand here to see past versions of factors2-9.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
1	Nfia	Club	9.476699
5	Foxq1	Goblet	-21.713513
6	Cdhr3	Ciliated	-6.302895
8	Muc5b	Club	14.528107
11	Krt4	Hillock	-29.114409
12	Krt13	Hillock	-8.894510
13	Krt8	Basal	-44.447667
14	Ecm1	Hillock	-23.139488
15	S100a11	Hillock	-42.664594
16	Cldn3	Hillock	-46.545916
17	Lgals3	Hillock	-50.948248
18	Anxa1	Hillock	-56.775524
36	Atp6v1c2	Ionocyte	5.813573

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0048519	negative regulation of biological proces…	4491	520	356.02	2.3e-24
GO:0048523	negative regulation of cellular process	4081	481	323.52	8.8e-24
GO:0006950	response to stress	2940	372	233.07	6.2e-23
GO:0006518	peptide metabolic process	700	133	55.49	5.6e-22
GO:0008219	cell death	1897	265	150.38	1.1e-21
GO:1901564	organonitrogen compound metabolic proces…	5378	581	426.34	2.9e-20
GO:0043603	cellular amide metabolic process	830	143	65.80	1.8e-19
GO:0048518	positive regulation of biological proces…	5006	542	396.85	1.2e-18
GO:0043043	peptide biosynthetic process	575	110	45.58	1.5e-18
GO:0006412	translation	554	107	43.92	2.3e-18

Factor 12

Expand here to see past versions of factors2-10.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
1	Nfia	Club	-9.433206
5	Foxq1	Goblet	24.314038
6	Cdhr3	Ciliated	-18.214837
8	Muc5b	Club	-14.773134
11	Krt4	Hillock	28.796426
12	Krt13	Hillock	5.814991
13	Krt8	Basal	43.847905
14	Ecm1	Hillock	19.461544
15	S100a11	Hillock	24.516852
16	Cldn3	Hillock	44.850683
17	Lgals3	Hillock	49.298476
18	Anxa1	Hillock	53.938434
26	Sox9	Tuft-2	-5.078661
36	Atp6v1c2	Ionocyte	-6.082813

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0010941	regulation of cell death	1553	256	156.40	1.4e-16
GO:0048523	negative regulation of cellular process	4081	549	411.00	9.5e-16
GO:0048519	negative regulation of biological proces…	4491	592	452.29	2.6e-15
GO:0042981	regulation of apoptotic process	1401	232	141.10	2.9e-15
GO:0043067	regulation of programmed cell death	1418	234	142.81	3.2e-15
GO:0008219	cell death	1897	293	191.05	4.6e-15
GO:0043066	negative regulation of apoptotic process	823	155	82.88	4.7e-15
GO:0043069	negative regulation of programmed cell d…	839	157	84.50	5.5e-15
GO:0060548	negative regulation of cell death	932	168	93.86	1.9e-14
GO:0012501	programmed cell death	1752	272	176.45	3.0e-14

Factor 14

Expand here to see past versions of factors2-11.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
4	Ascl3	Ionocyte	-30.58022
37	Atp6v0d2	Ionocyte	-33.64109
38	Cftr	Ionocyte	-24.75583

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0055067	monovalent inorganic cation homeostasis	137	7	0.49	5.7e-07
GO:0050801	ion homeostasis	673	13	2.41	5.9e-07
GO:0048878	chemical homeostasis	961	14	3.44	5.7e-06
GO:0055080	cation homeostasis	604	11	2.16	8.6e-06
GO:0098771	inorganic ion homeostasis	620	11	2.22	1.1e-05
GO:0006821	chloride transport	89	5	0.32	1.6e-05
GO:0030004	cellular monovalent inorganic cation hom…	97	5	0.35	2.5e-05
GO:0007588	excretion	50	4	0.18	3.0e-05
GO:0065008	regulation of biological quality	3110	25	11.14	3.1e-05
GO:0046068	cGMP metabolic process	55	4	0.20	4.4e-05

Factor 15

Expand here to see past versions of factors2-12.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0018979	trichloroethylene metabolic process	1	1	0.00	0.00012
GO:0018931	naphthalene metabolic process	2	1	0.00	0.00023
GO:0042196	chlorinated hydrocarbon metabolic proces…	2	1	0.00	0.00023
GO:0042197	halogenated hydrocarbon metabolic proces…	2	1	0.00	0.00023
GO:0090420	naphthalene-containing compound metaboli…	2	1	0.00	0.00023
GO:0019373	epoxygenase P450 pathway	20	1	0.00	0.00231
GO:0006805	xenobiotic metabolic process	43	1	0.00	0.00496
GO:0019369	arachidonic acid metabolic process	43	1	0.00	0.00496
GO:0071466	cellular response to xenobiotic stimulus	47	1	0.01	0.00542
GO:0009410	response to xenobiotic stimulus	53	1	0.01	0.00612

Factor 16

Expand here to see past versions of factors2-13.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0007049	cell cycle	1476	36	4.18	1.9e-28
GO:1903047	mitotic cell cycle process	567	23	1.61	1.2e-21
GO:0000278	mitotic cell cycle	733	24	2.08	1.8e-20
GO:0022402	cell cycle process	947	24	2.68	6.7e-18
GO:0051301	cell division	526	19	1.49	8.7e-17
GO:0006260	DNA replication	243	15	0.69	1.1e-16
GO:0006261	DNA-dependent DNA replication	120	12	0.34	5.2e-16
GO:0006259	DNA metabolic process	820	21	2.32	1.3e-15
GO:0006270	DNA replication initiation	30	8	0.08	1.3e-14
GO:0051276	chromosome organization	990	21	2.80	5.5e-14

Factor 18

Expand here to see past versions of factors2-14.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
7	Rgs13	Tuft	21.452246
21	Alox5ap	Tuft-2	21.147165
24	Gfi1b	Tuft-2	9.272023
25	Spib	Tuft-2	10.512412
26	Sox9	Tuft-2	5.933583

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0001580	detection of chemical stimulus involved …	29	8	0.13	3.8e-13
GO:0050913	sensory perception of bitter taste	32	8	0.14	9.1e-13
GO:0050909	sensory perception of taste	51	9	0.22	9.8e-13
GO:0050912	detection of chemical stimulus involved …	33	8	0.14	1.2e-12
GO:0050907	detection of chemical stimulus involved …	45	8	0.20	1.8e-11
GO:0050906	detection of stimulus involved in sensor…	105	9	0.46	8.0e-10
GO:0009593	detection of chemical stimulus	71	8	0.31	8.1e-10
GO:0007606	sensory perception of chemical stimulus	141	9	0.62	1.1e-08
GO:0007600	sensory perception	511	14	2.24	4.1e-08
GO:0051606	detection of stimulus	193	9	0.85	1.7e-07

Factor 20

Expand here to see past versions of factors2-15.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0071594	thymocyte aggregation	2	2	0.02	0.00010
GO:0072535	tumor necrosis factor (ligand) superfami…	2	2	0.02	0.00010
GO:2000307	regulation of tumor necrosis factor (lig…	2	2	0.02	0.00010
GO:2000309	positive regulation of tumor necrosis fa…	2	2	0.02	0.00010
GO:0007099	centriole replication	27	4	0.27	0.00015
GO:0098534	centriole assembly	28	4	0.28	0.00017
GO:0001807	regulation of type IV hypersensitivity	3	2	0.03	0.00030
GO:0070489	T cell aggregation	3	2	0.03	0.00030
GO:0051298	centrosome duplication	61	5	0.62	0.00038
GO:0046599	regulation of centriole replication	15	3	0.15	0.00042

Factor 21

Expand here to see past versions of factors2-16.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
11	Krt4	Hillock	-11.26243
12	Krt13	Hillock	-30.80692
14	Ecm1	Hillock	-12.42475

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0031424	keratinization	33	9	0.23	9.2e-13
GO:0043588	skin development	259	15	1.80	3.3e-10
GO:0030216	keratinocyte differentiation	122	11	0.85	8.2e-10
GO:0008544	epidermis development	287	14	1.99	1.2e-08
GO:0045104	intermediate filament cytoskeleton organ…	42	7	0.29	1.4e-08
GO:0050891	multicellular organismal water homeostas…	42	7	0.29	1.4e-08
GO:0045103	intermediate filament-based process	43	7	0.30	1.7e-08
GO:0030104	water homeostasis	45	7	0.31	2.4e-08
GO:0030855	epithelial cell differentiation	545	18	3.78	3.9e-08
GO:0009913	epidermal cell differentiation	182	11	1.26	5.5e-08

Factor 23

Expand here to see past versions of factors2-17.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
4	Ascl3	Ionocyte	-8.357358

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0002376	immune system process	1951	62	20.07	7.3e-17
GO:0006955	immune response	1060	43	10.90	3.9e-15
GO:1903039	positive regulation of leukocyte cell-ce…	169	18	1.74	1.4e-13
GO:0007159	leukocyte cell-cell adhesion	305	22	3.14	7.6e-13
GO:0022409	positive regulation of cell-cell adhesio…	202	18	2.08	3.0e-12
GO:0002682	regulation of immune system process	1073	39	11.04	3.1e-12
GO:0046649	lymphocyte activation	599	29	6.16	3.3e-12
GO:0045321	leukocyte activation	707	31	7.27	7.0e-12
GO:0050870	positive regulation of T cell activation	159	16	1.64	8.1e-12
GO:1903037	regulation of leukocyte cell-cell adhesi…	277	20	2.85	8.8e-12

Factor 24

Expand here to see past versions of factors2-18.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0003341	cilium movement	69	3	0.07	4.0e-05
GO:0007018	microtubule-based movement	242	4	0.24	7.7e-05
GO:0060271	cilium assembly	272	4	0.27	0.00012
GO:0044782	cilium organization	291	4	0.29	0.00016
GO:0021591	ventricular system development	32	2	0.03	0.00044
GO:0120031	plasma membrane bounded cell projection …	443	4	0.44	0.00077
GO:0030031	cell projection assembly	450	4	0.44	0.00082
GO:0061886	negative regulation of mini excitatory p…	1	1	0.00	0.00098
GO:0099149	regulation of postsynaptic neurotransmit…	1	1	0.00	0.00098
GO:1903353	regulation of nucleus organization	1	1	0.00	0.00098

Factor 26

Expand here to see past versions of factors2-19.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0042403	thyroid hormone metabolic process	22	6	0.13	2.4e-09
GO:0006590	thyroid hormone generation	13	5	0.08	7.6e-09
GO:0018958	phenol-containing compound metabolic pro…	94	8	0.55	7.5e-08
GO:0006575	cellular modified amino acid metabolic p…	146	9	0.85	1.8e-07
GO:0042445	hormone metabolic process	144	8	0.84	2.0e-06
GO:0071675	regulation of mononuclear cell migration	41	4	0.24	9.4e-05
GO:0036343	psychomotor behavior	3	2	0.02	0.00010
GO:0061744	motor behavior	4	2	0.02	0.00020
GO:0065008	regulation of biological quality	3110	33	18.15	0.00026
GO:0090025	regulation of monocyte chemotaxis	22	3	0.13	0.00027

Factor 27

Expand here to see past versions of factors2-20.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
25	Spib	Tuft-2	25.377272
27	Gp2	Goblet	8.869902

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0002376	immune system process	1951	41	17.25	8.0e-08
GO:0006952	defense response	1161	29	10.26	3.1e-07
GO:0045087	innate immune response	558	19	4.93	5.0e-07
GO:0006955	immune response	1060	27	9.37	5.8e-07
GO:0006954	inflammatory response	552	17	4.88	8.0e-06
GO:0097530	granulocyte migration	113	7	1.00	6.5e-05
GO:0042554	superoxide anion generation	28	4	0.25	0.00010
GO:0006801	superoxide metabolic process	55	5	0.49	0.00012
GO:1901292	nucleoside phosphate catabolic process	56	5	0.50	0.00013
GO:1990266	neutrophil migration	93	6	0.82	0.00018

Factor 28

Expand here to see past versions of factors2-21.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
7	Rgs13	Tuft	9.246186
19	Il25	Tuft	-16.165490
21	Alox5ap	Tuft-2	12.537995
24	Gfi1b	Tuft-2	8.808959

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0050912	detection of chemical stimulus involved …	33	15	0.26	1.1e-23
GO:0001580	detection of chemical stimulus involved …	29	14	0.23	1.2e-22
GO:0050913	sensory perception of bitter taste	32	14	0.25	7.2e-22
GO:0050907	detection of chemical stimulus involved …	45	15	0.35	3.4e-21
GO:0050909	sensory perception of taste	51	15	0.40	3.1e-20
GO:0009593	detection of chemical stimulus	71	15	0.56	7.7e-18
GO:0050906	detection of stimulus involved in sensor…	105	16	0.83	1.5e-16
GO:0007606	sensory perception of chemical stimulus	141	15	1.11	3.2e-13
GO:0051606	detection of stimulus	193	16	1.52	2.5e-12
GO:0007186	G-protein coupled receptor signaling pat…	685	25	5.38	1.2e-10

Factor 29

Expand here to see past versions of factors2-22.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
25	Spib	Tuft-2	-56.63392

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0002376	immune system process	1951	55	17.59	2.2e-15
GO:0045321	leukocyte activation	707	28	6.37	3.5e-11
GO:0001775	cell activation	821	30	7.40	4.5e-11
GO:0006955	immune response	1060	33	9.55	2.8e-10
GO:0002521	leukocyte differentiation	489	22	4.41	5.3e-10
GO:0046649	lymphocyte activation	599	24	5.40	8.3e-10
GO:0002682	regulation of immune system process	1073	32	9.67	1.6e-09
GO:0002684	positive regulation of immune system pro…	735	25	6.63	9.9e-09
GO:0002696	positive regulation of leukocyte activat…	259	15	2.33	1.3e-08
GO:0051251	positive regulation of lymphocyte activa…	225	14	2.03	1.6e-08

Factor 30

Expand here to see past versions of factors2-23.png:

Version	Author	Date
89558d3	Jason Willwerscheid	2018-12-04

Significant genes that are also mentioned in the paper:

	gene	type	t.val
6	Cdhr3	Ciliated	13.775604
18	Anxa1	Hillock	-6.524072

Gene Ontology terms:

GO.ID	Term	Annotated	Significant	Expected	classic
GO:0044782	cilium organization	291	47	12.12	1.1e-15
GO:0060271	cilium assembly	272	44	11.33	8.3e-15
GO:0120031	plasma membrane bounded cell projection …	443	49	18.46	4.5e-10
GO:0007017	microtubule-based process	639	62	26.62	4.8e-10
GO:0030031	cell projection assembly	450	49	18.75	7.8e-10
GO:0003341	cilium movement	69	17	2.87	2.2e-09
GO:0035082	axoneme assembly	60	15	2.50	1.6e-08
GO:0001578	microtubule bundle formation	88	17	3.67	1.1e-07
GO:0007018	microtubule-based movement	242	29	10.08	3.2e-07
GO:0000226	microtubule cytoskeleton organization	457	43	19.04	5.6e-07

Session information

sessionInfo()
#> R version 3.4.3 (2017-11-30)
#> Platform: x86_64-apple-darwin15.6.0 (64-bit)
#> Running under: macOS High Sierra 10.13.6
#> 
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
#> [8] methods   base     
#> 
#> other attached packages:
#>  [1] org.Mm.eg.db_3.5.0   topGO_2.30.1         SparseM_1.77        
#>  [4] GO.db_3.5.0          AnnotationDbi_1.40.0 IRanges_2.12.0      
#>  [7] S4Vectors_0.16.0     Biobase_2.38.0       graph_1.56.0        
#> [10] BiocGenerics_0.24.0  ggplot2_3.1.0       
#> 
#> loaded via a namespace (and not attached):
#>  [1] xfun_0.4           lattice_0.20-35    colorspace_1.3-2  
#>  [4] htmltools_0.3.6    yaml_2.2.0         blob_1.1.0        
#>  [7] rlang_0.3.0.1      R.oo_1.21.0        pillar_1.2.1      
#> [10] glue_1.3.0         withr_2.1.2.9000   DBI_0.7           
#> [13] R.utils_2.6.0      bit64_0.9-7        bindrcpp_0.2      
#> [16] matrixStats_0.52.2 bindr_0.1          plyr_1.8.4        
#> [19] stringr_1.3.1      munsell_0.5.0      gtable_0.2.0      
#> [22] workflowr_1.0.1    flashier_0.1.0     R.methodsS3_1.7.1 
#> [25] evaluate_0.12      memoise_1.1.0      labeling_0.3      
#> [28] knitr_1.20.22      highr_0.7          Rcpp_1.0.0        
#> [31] scales_1.0.0       backports_1.1.2    bit_1.1-12        
#> [34] digest_0.6.18      stringi_1.2.4      dplyr_0.7.4       
#> [37] grid_3.4.3         rprojroot_1.3-2    tools_3.4.3       
#> [40] magrittr_1.5       lazyeval_0.2.1     tibble_1.4.2      
#> [43] RSQLite_2.0        whisker_0.3-2      pkgconfig_2.0.1   
#> [46] assertthat_0.2.0   rmarkdown_1.8      R6_2.3.0          
#> [49] git2r_0.21.0       compiler_3.4.3