Coexpression cluster:C3659

Full id: C3659_breast_MCF7_cerebellum_occipital_pons_frontal_paracentral

Phase1 CAGE Peaks

Hg19::chr17:57184170..57184257,-	p1@TRIM37
Hg19::chr17:57184260..57184271,-	p6@TRIM37
Hg19::chr20:49411484..49411518,+	p2@BCAS4

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:0005777	peroxisome	0.0499682941000963
GO:0042579	microbody	0.0499682941000963

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
central nervous system	2.73e-31	82
regional part of nervous system	3.00e-31	94
nervous system	3.00e-31	94
neural tube	6.31e-27	57
neural rod	6.31e-27	57
future spinal cord	6.31e-27	57
neural keel	6.31e-27	57
brain	1.83e-26	69
future brain	1.83e-26	69
neurectoderm	2.58e-23	90
regional part of forebrain	4.83e-23	41
forebrain	4.83e-23	41
future forebrain	4.83e-23	41
regional part of brain	4.93e-23	59
neural plate	7.66e-23	86
presumptive neural plate	7.66e-23	86
anterior neural tube	1.88e-22	42
ectoderm	3.63e-21	173
presumptive ectoderm	3.63e-21	173
ectoderm-derived structure	1.49e-20	169
telencephalon	7.07e-20	34
gray matter	7.15e-20	34
brain grey matter	7.15e-20	34
cerebral hemisphere	1.36e-19	32
regional part of telencephalon	3.17e-19	33
pre-chordal neural plate	4.32e-18	61
anterior region of body	2.50e-17	129
craniocervical region	2.50e-17	129
head	4.57e-17	123
cerebral cortex	2.11e-15	25
pallium	2.11e-15	25
regional part of cerebral cortex	8.81e-15	22
neocortex	1.41e-13	20
adult organism	2.29e-13	115
tube	5.21e-08	194
organism subdivision	3.12e-07	365
multi-tissue structure	7.73e-07	347

Disease

Ontology term	p-value	n
cell type cancer	8.19e-12	143
carcinoma	3.80e-10	106

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	2	14.9754496840058	0.00576829454079388	0.0259547160202478
BCL3#602	2	23.0314018691589	0.00246467476084291	0.0138503183937408
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296225638618499
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189855063120404
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115146946200872
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279179501749726
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171602978850618
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321757380783663
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032028151367675
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461726143401244
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00761509894100643
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153962874908271
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390903895724204
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108614595546338
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122752633772038
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127937931584248
NFE2#4778	2	51.469507101086	0.000498765352839211	0.00440623876545207
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172781180893036
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881530396217038
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.0108927584226531
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276359325803793
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00202925632048777
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308807202213936
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246230295625896
SP2#6668	2	17.4356869958964	0.00427356848176974	0.02031437889343
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287505828873878
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00628852127191072
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390066800155975
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00615008253217109
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329034520192163
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190077931396696
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328949350562708
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156338043555685
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242598520602994

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.