Coexpression cluster:C4240

Full id: C4240_Dendritic_left_mature_heart_medial_occipital_Macrophage

Phase1 CAGE Peaks

Hg19::chr2:63816087..63816124,+	p1@MDH1
Hg19::chr2:63816126..63816152,+	p2@MDH1
Hg19::chr2:63816295..63816356,+	p4@MDH1

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
central nervous system	2.71e-16	82
brain	5.07e-15	69
future brain	5.07e-15	69
neural tube	1.68e-14	57
neural rod	1.68e-14	57
future spinal cord	1.68e-14	57
neural keel	1.68e-14	57
regional part of nervous system	6.10e-14	94
nervous system	6.10e-14	94
regional part of brain	9.44e-14	59
regional part of forebrain	1.88e-13	41
forebrain	1.88e-13	41
future forebrain	1.88e-13	41
anterior neural tube	1.35e-12	42
cerebral hemisphere	9.01e-12	32
gray matter	1.12e-11	34
brain grey matter	1.12e-11	34
telencephalon	2.85e-11	34
regional part of telencephalon	1.09e-10	33
neural plate	4.55e-10	86
presumptive neural plate	4.55e-10	86
regional part of cerebral cortex	1.05e-09	22
neurectoderm	1.75e-09	90
cerebral cortex	6.29e-09	25
pallium	6.29e-09	25
neocortex	8.10e-09	20
head	2.12e-08	123
anterior region of body	2.53e-08	129
craniocervical region	2.53e-08	129
adult organism	5.84e-08	115
ectoderm-derived structure	1.08e-07	169
pre-chordal neural plate	1.21e-07	61
ectoderm	2.03e-07	173
presumptive ectoderm	2.03e-07	173

Disease

Ontology term	p-value	n
disease of cellular proliferation	2.89e-08	239
cancer	1.22e-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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.0012985779870187
BCL11A#53335	2	18.9129700690714	0.00363940624837968	0.018392332777244
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139394433250752
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115521135066832
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661713220276183
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326385775533846
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437951607222766
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463625208975968
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167874772672933
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000678213879950348
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763817966117517
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.0010740661797076
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154493614997268
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434909921141439
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000758437567121252
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00136981300584119
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.000681291770343769
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157142270157165
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295296162460531
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270192613199862
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00200009196285924
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381419431311513
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000605649859506726
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00137000218040352
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00883783797025364
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277568165385034
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00240025320410135
SMARCC2#6601	3	94.1553744268976	1.19621075407887e-06	4.8592397878352e-05
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247168459579626
SRF#6722	3	13.7971782621678	0.000380661502580019	0.0037580023317851
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544425678675737
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00615496503404587
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197501066402581
WRNIP1#56897	3	109.819964349376	7.53682839543883e-07	3.32969044327934e-05
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330230795386415
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243251911299265
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389923991481769
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109704179682475

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.