Coexpression cluster:C4685

Full id: C4685_medial_frontal_amygdala_parietal_paracentral_occipital_Fibroblast

Phase1 CAGE Peaks

Hg19::chr7:35840659..35840671,+	p3@SEPT7
Hg19::chr7:35840681..35840693,+	p2@SEPT7
Hg19::chr7:35840743..35840750,+	p4@SEPT7

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

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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

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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>

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Cell Type

Ontology term	p-value	n
fibroblast	2.10e-07	75

Uber Anatomy

Ontology term	p-value	n
adult organism	2.55e-16	115
neural tube	3.02e-15	57
neural rod	3.02e-15	57
future spinal cord	3.02e-15	57
neural keel	3.02e-15	57
regional part of brain	4.55e-15	59
central nervous system	5.07e-14	82
brain	5.88e-14	69
future brain	5.88e-14	69
anterior neural tube	6.67e-14	42
telencephalon	1.06e-13	34
regional part of forebrain	1.10e-13	41
forebrain	1.10e-13	41
future forebrain	1.10e-13	41
gray matter	1.48e-13	34
brain grey matter	1.48e-13	34
regional part of telencephalon	4.47e-13	33
cerebral hemisphere	9.12e-13	32
regional part of nervous system	1.87e-10	94
nervous system	1.87e-10	94
neural plate	1.20e-09	86
presumptive neural plate	1.20e-09	86
regional part of cerebral cortex	3.73e-09	22
neurectoderm	8.71e-09	90
cerebral cortex	8.74e-09	25
pallium	8.74e-09	25
head	1.91e-08	123
anterior region of body	2.10e-08	129
craniocervical region	2.10e-08	129
neocortex	4.68e-08	20
basal ganglion	5.96e-07	9
nuclear complex of neuraxis	5.96e-07	9
aggregate regional part of brain	5.96e-07	9
collection of basal ganglia	5.96e-07	9
cerebral subcortex	5.96e-07	9
pre-chordal neural plate	7.52e-07	61

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164528961904768
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191127893749825
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662782374056749
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327705117255826
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324280968083927
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322454037165704
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464915933909016
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256383033516347
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00765209537310848
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000372707368243414
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.0058417407307166
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000629785461194334
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435961153685635
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109198645199181
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128724723168777
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187421870268493
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00195444194822266
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00723392260895371
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029605923244872
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270829641394564
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00310185412485753
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173667762835649
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885708265393422
REST#5978	3	9.65002871612802	0.00111263624711459	0.00771290435499805
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00204059160062361
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545701277735427
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631964576761565
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.00064921150746222
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331235780899877
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000634853381036177
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110128567224767

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

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This analysis result is provided for C0 - C305 clusters.