Coexpression cluster:C2783

Full id: C2783_medulla_optic_blood_Whole_Hepatocyte_substantia_corpus

Phase1 CAGE Peaks

Hg19::chr4:170947459..170947472,-	p4@MFAP3L
Hg19::chr4:170947485..170947499,-	p2@MFAP3L
Hg19::chr4:170947522..170947563,-	p1@MFAP3L
Hg19::chr4:170947565..170947583,-	p3@MFAP3L

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	1.14e-39	115
regional part of nervous system	1.93e-29	94
nervous system	1.93e-29	94
neural tube	9.56e-29	57
neural rod	9.56e-29	57
future spinal cord	9.56e-29	57
neural keel	9.56e-29	57
central nervous system	6.23e-28	82
regional part of brain	1.33e-23	59
brain	2.01e-23	69
future brain	2.01e-23	69
anterior neural tube	1.12e-22	42
regional part of forebrain	1.91e-22	41
forebrain	1.91e-22	41
future forebrain	1.91e-22	41
neural plate	4.31e-22	86
presumptive neural plate	4.31e-22	86
neurectoderm	6.90e-21	90
telencephalon	7.38e-19	34
gray matter	8.47e-19	34
brain grey matter	8.47e-19	34
regional part of telencephalon	3.11e-18	33
cerebral hemisphere	1.71e-17	32
pre-chordal neural plate	4.72e-17	61
ectoderm-derived structure	1.39e-16	169
ectoderm	4.66e-16	173
presumptive ectoderm	4.66e-16	173
head	4.81e-15	123
anterior region of body	6.11e-14	129
craniocervical region	6.11e-14	129
cerebral cortex	2.23e-13	25
pallium	2.23e-13	25
regional part of cerebral cortex	2.42e-12	22
organism subdivision	2.37e-11	365
neocortex	3.11e-11	20
tube	5.30e-10	194
anatomical conduit	1.10e-08	241
multi-cellular organism	3.04e-08	659
posterior neural tube	2.84e-07	15
chordal neural plate	2.84e-07	15
nucleus of brain	5.85e-07	9
neural nucleus	5.85e-07	9
basal ganglion	8.62e-07	9
nuclear complex of neuraxis	8.62e-07	9
aggregate regional part of brain	8.62e-07	9
collection of basal ganglia	8.62e-07	9
cerebral subcortex	8.62e-07	9

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	4	6.33620157696263	0.000620310058721564	0.00513185695681412
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00819134908130283
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106718332729082
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00998588420027442
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101602425189111
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161188353663483
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186472126427578
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307978098040956
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00392253592525444
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.000794990143376481
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444646681400962
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129781512454639
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00685366017202364
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323019485533728
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115658050193719
YY1#7528	4	4.91117074985386	0.0017187183805544	0.010700520354499

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.