Coexpression cluster:C4588

Full id: C4588_neuroblastoma_neuroectodermal_osteosarcoma_medulloblastoma_acute_mesothelioma_small

Phase1 CAGE Peaks

Hg19::chr6:30525051..30525063,+	p3@PRR3
Hg19::chr6:30525064..30525098,+	p1@PRR3
Hg19::chr6:30525100..30525120,+	p2@PRR3

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>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
neural cell	9.80e-07	25

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	6.47e-16	94
nervous system	6.47e-16	94
central nervous system	3.19e-13	82
neurectoderm	1.94e-12	90
brain	2.82e-11	69
future brain	2.82e-11	69
neural plate	9.54e-11	86
presumptive neural plate	9.54e-11	86
neural tube	2.43e-09	57
neural rod	2.43e-09	57
future spinal cord	2.43e-09	57
neural keel	2.43e-09	57
ectoderm	5.35e-09	173
presumptive ectoderm	5.35e-09	173
pre-chordal neural plate	2.78e-08	61
regional part of brain	4.76e-08	59
regional part of cerebral cortex	4.79e-08	22
ectoderm-derived structure	8.35e-08	169
neocortex	1.06e-07	20
regional part of forebrain	1.12e-07	41
forebrain	1.12e-07	41
future forebrain	1.12e-07	41
cerebral cortex	1.15e-07	25
pallium	1.15e-07	25
anterior neural tube	3.37e-07	42
cerebral hemisphere	4.10e-07	32
telencephalon	6.67e-07	34
anterior region of body	8.88e-07	129
craniocervical region	8.88e-07	129
head	9.28e-07	123

Disease

Ontology term	p-value	n
cancer	1.31e-34	235
disease of cellular proliferation	4.52e-34	239
cell type cancer	1.79e-17	143
organ system cancer	1.57e-14	137
hematologic cancer	2.36e-14	51
immune system cancer	2.36e-14	51
leukemia	3.32e-12	39
carcinoma	1.98e-11	106
myeloid leukemia	6.31e-09	31

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	0.00129986080467452
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139451136071057
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662549655526532
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324052225336631
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322207078417779
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464628485456079
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256302232056051
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.0076484827294441
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00583774106037986
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107638276059127
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154744167027868
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039324995893397
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000760012723023892
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187304466311789
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722847761451697
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295844220700321
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270690397362998
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000606137893237191
REST#5978	3	9.65002871612802	0.00111263624711459	0.0077088109998939
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.004864782957867
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165906211415237
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278082786962522
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00240273308917045
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109380230280452
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00376226996006005
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197934077266801
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191053745946537
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422817910372265
WRNIP1#56897	3	109.819964349376	7.53682839543883e-07	3.33250982553444e-05
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331036780731118
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140810826658104
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110031827443297

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.