Coexpression cluster:C779

Full id: C779_testis_medial_occipital_brain_temporal_postcentral_insula

Phase1 CAGE Peaks

Hg19::chr10:134145640..134145724,+	p1@LRRC27
Hg19::chr11:72504681..72504716,-	p6@STARD10
Hg19::chr11:73882263..73882276,+	p5@PPME1
Hg19::chr11:73882283..73882309,+	p3@PPME1
Hg19::chr12:121341939..121341985,-	p3@SPPL3
Hg19::chr12:50101500..50101550,+	p23@TMBIM6
Hg19::chr13:37006398..37006417,+	p5@CCNA1
Hg19::chr14:105767100..105767153,+	p3@PACS2
Hg19::chr15:33486929..33486977,-	p5@FMN1
Hg19::chr9:34665983..34666063,-	p1@ENST00000416454 p1@ENST00000421828 p1@ENST00000544078 p1@ENST00000556719

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:0051722	protein C-terminal methylesterase activity	0.00735856827869091
GO:0051723	protein methylesterase activity	0.00735856827869091
GO:0006482	protein amino acid demethylation	0.00735856827869091
GO:0008214	protein amino acid dealkylation	0.00735856827869091
GO:0007141	male meiosis I	0.00882976206266084
GO:0051721	protein phosphatase 2A binding	0.00981026913500083
GO:0007140	male meiosis	0.0147128048027599
GO:0019903	protein phosphatase binding	0.0312463083769772
GO:0019902	phosphatase binding	0.0359328864606653
GO:0004864	protein phosphatase inhibitor activity	0.0428416640546203
GO:0019212	phosphatase inhibitor activity	0.0428416640546203
GO:0008601	protein phosphatase type 2A regulator activity	0.0428416640546203

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
nervous system	5.77e-37	89
central nervous system	2.77e-36	81
neural tube	1.15e-35	56
neural rod	1.15e-35	56
future spinal cord	1.15e-35	56
neural keel	1.15e-35	56
regional part of nervous system	9.15e-34	53
regional part of brain	9.15e-34	53
brain	5.58e-32	68
future brain	5.58e-32	68
neurectoderm	3.24e-31	86
neural plate	5.45e-30	82
presumptive neural plate	5.45e-30	82
adult organism	1.39e-29	114
regional part of forebrain	2.42e-26	41
forebrain	2.42e-26	41
anterior neural tube	2.42e-26	41
future forebrain	2.42e-26	41
ectoderm-derived structure	1.12e-23	171
ectoderm	1.12e-23	171
presumptive ectoderm	1.12e-23	171
telencephalon	4.60e-22	34
brain grey matter	6.65e-22	34
gray matter	6.65e-22	34
pre-chordal neural plate	9.75e-22	61
ecto-epithelium	1.66e-21	104
cerebral hemisphere	7.85e-21	32
regional part of telencephalon	1.15e-20	32
structure with developmental contribution from neural crest	1.16e-19	132
cerebral cortex	2.74e-16	25
pallium	2.74e-16	25
regional part of cerebral cortex	4.39e-16	22
anatomical cluster	7.01e-16	373
organ system subdivision	1.37e-15	223
neocortex	9.77e-15	20
tube	2.26e-12	192
multi-cellular organism	6.64e-11	656
multi-tissue structure	1.01e-10	342
anatomical conduit	1.04e-10	240
posterior neural tube	2.54e-10	15
chordal neural plate	2.54e-10	15
epithelium	4.80e-10	306
cell layer	7.12e-10	309
organ part	3.20e-09	218
segmental subdivision of hindbrain	1.46e-08	12
hindbrain	1.46e-08	12
presumptive hindbrain	1.46e-08	12
segmental subdivision of nervous system	6.95e-08	13
anatomical system	1.93e-07	624
anatomical group	2.05e-07	625
basal ganglion	3.28e-07	9
nuclear complex of neuraxis	3.28e-07	9
aggregate regional part of brain	3.28e-07	9
collection of basal ganglia	3.28e-07	9
cerebral subcortex	3.28e-07	9
embryo	3.84e-07	592
neural nucleus	4.50e-07	9
nucleus of brain	4.50e-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
ATF3#467	4	8.9852698104035	0.000663674601877764	0.00542613995189539
BRCA1#672	3	6.05526919296713	0.0112162556013866	0.0411860811037627
CHD2#1106	6	6.20641370047011	0.000121334130924711	0.001643794953904
CTCFL#140690	3	5.92394230769231	0.0119085785576893	0.0433336830070909
E2F1#1869	7	3.43517245041553	0.000973185478914308	0.00699604338052942
E2F4#1874	5	6.33403015764222	0.000550156721856872	0.00469848866415978
E2F6#1876	9	4.51544015852765	4.07099158370721e-06	0.000129546096895429
EGR1#1958	6	2.99290745688608	0.00644658718507573	0.0280087827199486
ELF1#1997	7	2.98066857116528	0.00237820287046913	0.0134709366302704
GATA3#2625	3	8.1709549071618	0.00488857399967495	0.0228754773937924
IRF1#3659	7	5.34601462749473	5.49768438584683e-05	0.000930587778887289
MAX#4149	6	3.87153330540427	0.00164960278647382	0.0103163392464994
MXI1#4601	4	3.98462865150372	0.0129656298253104	0.0460114649448043
MYC#4609	7	3.65559731012658	0.00065450084012841	0.00535994771757006
NANOG#79923	3	8.7734335443038	0.00400236077424559	0.0191876317145483
NRF1#4899	5	6.10513972385545	0.000652726297463064	0.00534583451856532
PAX5#5079	6	4.0017393187067	0.00137948966176299	0.00898599892626862
PRDM1#639	2	26.3661911554922	0.00248496252103967	0.0139553154129624
RAD21#5885	4	4.14201355818253	0.0113227647567404	0.0415275399785508
RDBP#7936	2	30.727680798005	0.00183992044924957	0.0108878379397799
RFX5#5993	5	6.02395541359755	0.000694511406874844	0.00559676518692916
SIN3A#25942	6	3.24533083608908	0.00422384063048573	0.0201008699356283
SMC3#9126	4	6.01797313797314	0.00295796391668531	0.0157688118776324
SP1#6667	7	3.98886696469863	0.000373436559150151	0.00371123235332407
STAT1#6772	3	6.21197624915976	0.0104584117795196	0.0387465792068552
TAF1#6872	7	2.3401324000217	0.0104083984434833	0.0386298054384843
THAP1#55145	3	9.4107433808554	0.00328318355314289	0.0170009622245372
USF1#7391	6	3.81689956632477	0.00178092866379164	0.010926942117127
USF2#7392	4	5.19687895402784	0.00504600384015446	0.023504731950488
YY1#7528	6	2.94670244991231	0.00698724787395188	0.0295358068849986

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.