Coexpression cluster:C4745

Full id: C4745_CD19_CD14_stomach_immature_epididymis_spinal_smallcell

Phase1 CAGE Peaks

Hg19::chr8:24151557..24151590,+	p1@ADAM28
Hg19::chr8:24151592..24151611,+	p2@ADAM28
Hg19::chr8:24162989..24162994,+	p@chr8:24162989..24162994 +

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

---

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

---

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

---

Cell Type

Ontology term	p-value	n
defensive cell	1.48e-23	48
phagocyte	1.48e-23	48
hematopoietic stem cell	1.31e-22	168
angioblastic mesenchymal cell	1.31e-22	168
leukocyte	1.62e-22	136
macrophage dendritic cell progenitor	1.70e-22	61
myeloid cell	2.05e-21	108
common myeloid progenitor	2.05e-21	108
monopoietic cell	4.87e-21	59
monocyte	4.87e-21	59
monoblast	4.87e-21	59
promonocyte	4.87e-21	59
myeloid leukocyte	1.39e-20	72
hematopoietic oligopotent progenitor cell	2.18e-20	161
hematopoietic multipotent progenitor cell	2.18e-20	161
classical monocyte	3.80e-20	42
CD14-positive, CD16-negative classical monocyte	3.80e-20	42
granulocyte monocyte progenitor cell	8.63e-20	67
hematopoietic cell	1.77e-19	177
nongranular leukocyte	8.84e-19	115
myeloid lineage restricted progenitor cell	2.78e-17	66
hematopoietic lineage restricted progenitor cell	8.29e-16	120
B cell	5.33e-11	14
stuff accumulating cell	4.91e-08	87

Uber Anatomy

Ontology term	p-value	n
adult organism	8.23e-43	114
hematopoietic system	1.20e-19	98
blood island	1.20e-19	98
neural tube	1.31e-18	56
neural rod	1.31e-18	56
future spinal cord	1.31e-18	56
neural keel	1.31e-18	56
hemolymphoid system	8.47e-18	108
regional part of nervous system	6.22e-17	53
regional part of brain	6.22e-17	53
bone marrow	6.18e-16	76
regional part of forebrain	1.07e-15	41
forebrain	1.07e-15	41
anterior neural tube	1.07e-15	41
future forebrain	1.07e-15	41
immune system	3.18e-14	93
bone element	2.84e-13	82
neural plate	1.43e-12	82
presumptive neural plate	1.43e-12	82
central nervous system	1.54e-12	81
skeletal element	5.50e-12	90
brain grey matter	7.83e-12	34
gray matter	7.83e-12	34
telencephalon	1.08e-11	34
brain	1.71e-11	68
future brain	1.71e-11	68
neurectoderm	4.17e-11	86
regional part of telencephalon	1.02e-10	32
cerebral hemisphere	1.83e-10	32
pre-chordal neural plate	2.70e-10	61
nervous system	4.31e-10	89
skeletal system	1.64e-09	100
regional part of cerebral cortex	3.75e-09	22
neocortex	5.62e-08	20
cerebral cortex	3.02e-07	25
pallium	3.02e-07	25
ecto-epithelium	3.74e-07	104

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

---

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BATF#10538	2	16.2385345282024	0.00491746240780997	0.023006533907148
BCL11A#53335	2	18.9129700690714	0.00363940624837968	0.0183958933875968
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0226031516182987
IRF4#3662	2	14.6096751244961	0.00605612247321789	0.0268598341676747
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174621500962922

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

---

This analysis result is provided for C0 - C305 clusters.