Coexpression cluster:C3613

Full id: C3613_optic_Hep2_corpus_lens_Mesenchymal_globus_Chondrocyte

Phase1 CAGE Peaks

Hg19::chr17:20059323..20059342,+	p4@SPECC1
Hg19::chr17:20059346..20059355,+	p5@SPECC1
Hg19::chr17:20059358..20059401,+	p1@SPECC1

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.51e-17	253
endo-epithelial cell	1.55e-07	42

Uber Anatomy

Ontology term	p-value	n
central nervous system	6.94e-19	81
nervous system	8.35e-17	89
organ system subdivision	1.35e-15	223
neural tube	3.05e-15	56
neural rod	3.05e-15	56
future spinal cord	3.05e-15	56
neural keel	3.05e-15	56
brain	3.42e-15	68
future brain	3.42e-15	68
regional part of nervous system	7.55e-14	53
regional part of brain	7.55e-14	53
organ part	8.55e-13	218
ecto-epithelium	2.61e-12	104
ectoderm-derived structure	4.52e-12	171
ectoderm	4.52e-12	171
presumptive ectoderm	4.52e-12	171
neural plate	4.88e-12	82
presumptive neural plate	4.88e-12	82
brain grey matter	2.69e-11	34
gray matter	2.69e-11	34
telencephalon	3.32e-11	34
regional part of forebrain	7.15e-11	41
forebrain	7.15e-11	41
anterior neural tube	7.15e-11	41
future forebrain	7.15e-11	41
pre-chordal neural plate	2.46e-10	61
regional part of telencephalon	2.76e-10	32
neurectoderm	3.14e-10	86
cerebral hemisphere	4.04e-10	32
larynx	1.37e-07	9
cerebral cortex	1.45e-07	25
pallium	1.45e-07	25
multi-tissue structure	3.92e-07	342
regional part of cerebral cortex	6.94e-07	22
structure with developmental contribution from neural crest	7.22e-07	132

Disease

Ontology term	p-value	n
carcinoma	2.42e-12	106
cell type cancer	2.98e-09	143
reproductive organ cancer	2.65e-07	29
disease of cellular proliferation	2.78e-07	239
cancer	2.84e-07	235

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189811172084913
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324838013704494
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321644742546973
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320184011788953
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461631598426143
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.012791698905166
JUND#3727	3	6.99466394187103	0.00292184504273499	0.01565457212426
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00195011530266025
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294147104061997
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269317271599488
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172755740719163
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881418027779025
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.0020290165123667
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246165857113498
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542144565496928
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00628806584597852
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242571372156194
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388709497554471

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.