Coexpression cluster:C2238

Full id: C2238_cerebellum_spinal_occipital_parietal_putamen_medial_middle

Phase1 CAGE Peaks

Hg19::chr12:72058060..72058101,+	p5@THAP2
Hg19::chr7:64023410..64023428,-	p2@ZNF680
Hg19::chr7:64023441..64023462,-	p1@ZNF680
Hg19::chr7:64254793..64254813,+	p1@ZNF138

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

---

GO ID	GO name	FDR corrected p-value
GO:0003677	DNA binding	0.0403705274123335
GO:0008270	zinc ion binding	0.0403705274123335
GO:0046914	transition metal ion binding	0.0440143862349641
GO:0005634	nucleus	0.0472393264798422
GO:0003676	nucleic acid binding	0.0472393264798422
GO:0043169	cation binding	0.0472393264798422
GO:0046872	metal ion binding	0.0472393264798422
GO:0043167	ion binding	0.0472393264798422

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
lymphocyte	3.50e-10	53
common lymphoid progenitor	3.50e-10	53
lymphoid lineage restricted progenitor cell	9.23e-10	52

Uber Anatomy

Ontology term	p-value	n
adult organism	4.01e-33	115
central nervous system	7.40e-31	82
regional part of nervous system	1.91e-29	94
nervous system	1.91e-29	94
neural tube	1.63e-28	57
neural rod	1.63e-28	57
future spinal cord	1.63e-28	57
neural keel	1.63e-28	57
brain	6.25e-26	69
future brain	6.25e-26	69
regional part of forebrain	2.91e-24	41
forebrain	2.91e-24	41
future forebrain	2.91e-24	41
anterior neural tube	2.95e-24	42
regional part of brain	1.43e-23	59
neurectoderm	5.53e-22	90
neural plate	2.93e-21	86
presumptive neural plate	2.93e-21	86
gray matter	2.51e-20	34
brain grey matter	2.51e-20	34
telencephalon	4.18e-20	34
regional part of telencephalon	1.46e-19	33
cerebral hemisphere	5.90e-19	32
pre-chordal neural plate	8.12e-16	61
cerebral cortex	1.15e-14	25
pallium	1.15e-14	25
regional part of cerebral cortex	4.59e-14	22
anterior region of body	1.41e-13	129
craniocervical region	1.41e-13	129
ectoderm	3.04e-13	173
presumptive ectoderm	3.04e-13	173
neocortex	8.82e-13	20
ectoderm-derived structure	1.42e-12	169
head	2.54e-12	123
basal ganglion	3.29e-07	9
nuclear complex of neuraxis	3.29e-07	9
aggregate regional part of brain	3.29e-07	9
collection of basal ganglia	3.29e-07	9
cerebral subcortex	3.29e-07	9
nucleus of brain	3.64e-07	9
neural nucleus	3.64e-07	9

Disease

Ontology term	p-value	n
cancer	3.06e-10	235
disease of cellular proliferation	1.58e-09	239
organ system cancer	4.13e-08	137
hematologic cancer	7.98e-07	51
immune system cancer	7.98e-07	51

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
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436476967198784
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.0012893458275226
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109246926646688
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160658450619374
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234583501676353
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00389894915534791
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185668329188939
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00306992370981813
IRF3#3661	3	35.2364641586172	3.79279212646878e-05	0.000719555707350178
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508505721860695
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00618506018968863
PBX3#5090	3	16.4358845150581	0.000366943139555461	0.00365679146488863
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000825726703257416
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794909797400448
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00683332570797913
SP2#6668	3	19.6151478703835	0.000217100426924534	0.00248506701968121
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0280945568514746
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321491766199678
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243688445569524
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115194456465211
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279636303250057

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.