Coexpression cluster:C3917

Full id: C3917_pineal_thalamus_globus_spinal_substantia_caudate_locus

Phase1 CAGE Peaks

Hg19::chr1:197170611..197170660,+	p1@CRB1
Hg19::chr7:63767783..63767861,+	p2@ZNF736
Hg19::chr7:63767903..63767927,+	p4@ZNF736

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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GO ID	GO name	FDR corrected p-value
GO:0007163	establishment and/or maintenance of cell polarity	0.0236273009144786
GO:0016324	apical plasma membrane	0.0236273009144786
GO:0045177	apical part of cell	0.0236273009144786
GO:0050953	sensory perception of light stimulus	0.0367596844460144
GO:0007601	visual perception	0.0367596844460144

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	1.50e-36	114
neural tube	1.12e-30	56
neural rod	1.12e-30	56
future spinal cord	1.12e-30	56
neural keel	1.12e-30	56
regional part of nervous system	1.10e-28	53
regional part of brain	1.10e-28	53
brain	7.08e-26	68
future brain	7.08e-26	68
central nervous system	1.61e-24	81
regional part of forebrain	1.90e-24	41
forebrain	1.90e-24	41
anterior neural tube	1.90e-24	41
future forebrain	1.90e-24	41
neurectoderm	6.13e-24	86
nervous system	6.49e-24	89
neural plate	1.19e-22	82
presumptive neural plate	1.19e-22	82
brain grey matter	8.52e-20	34
gray matter	8.52e-20	34
telencephalon	9.28e-20	34
regional part of telencephalon	1.57e-18	32
cerebral hemisphere	1.72e-18	32
pre-chordal neural plate	5.12e-18	61
ecto-epithelium	2.94e-14	104
regional part of cerebral cortex	3.49e-14	22
cerebral cortex	4.60e-14	25
pallium	4.60e-14	25
ectoderm-derived structure	6.06e-13	171
ectoderm	6.06e-13	171
presumptive ectoderm	6.06e-13	171
neocortex	6.24e-13	20
structure with developmental contribution from neural crest	3.03e-11	132
organ system subdivision	9.23e-11	223
posterior neural tube	1.82e-07	15
chordal neural plate	1.82e-07	15
basal ganglion	2.73e-07	9
nuclear complex of neuraxis	2.73e-07	9
aggregate regional part of brain	2.73e-07	9
collection of basal ganglia	2.73e-07	9
cerebral subcortex	2.73e-07	9
neural nucleus	2.86e-07	9
nucleus of brain	2.86e-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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325544079236787
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322422298363947
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320818837297514
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462547158291712
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167548265784131
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00437004889887104
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000851485948319421
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186647920357656
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029467905839559
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.02697542322895
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471320454716622
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.017301048007633
REST#5978	3	9.65002871612802	0.00111263624711459	0.00767977113293243
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370779482052483
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246693094065966
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329133649368993
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329613472330771
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242924776598425
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109467693161369

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.