Coexpression cluster:C4603

Full id: C4603_non_acute_Hodgkin_chronic_Placental_thymus_rhabdomyosarcoma

Phase1 CAGE Peaks

Hg19::chr6:41909466..41909520,-	p1@CCND3
Hg19::chr6:41909533..41909560,-	p3@CCND3
Hg19::chr6:41909561..41909621,-	p4@CCND3

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
somatic cell	1.16e-11	591
native cell	6.57e-11	722
animal cell	6.76e-11	679
eukaryotic cell	6.76e-11	679
mesodermal cell	2.00e-10	119
contractile cell	1.38e-08	59
smooth muscle cell	7.33e-08	42
smooth muscle myoblast	7.33e-08	42
muscle precursor cell	1.67e-07	57
myoblast	1.67e-07	57
multi-potent skeletal muscle stem cell	1.67e-07	57
myeloid cell	1.81e-07	112
common myeloid progenitor	1.81e-07	112
muscle cell	2.54e-07	54
non-terminally differentiated cell	9.47e-07	180

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	5.07e-12	216
cardiovascular system	5.38e-10	110
circulatory system	8.93e-10	113
splanchnic layer of lateral plate mesoderm	1.78e-08	84
vasculature	2.99e-08	79
vascular system	2.99e-08	79
blood vessel	6.68e-08	60
epithelial tube open at both ends	6.68e-08	60
blood vasculature	6.68e-08	60
vascular cord	6.68e-08	60
epithelial tube	2.27e-07	118
vessel	3.39e-07	69

Disease

Ontology term	p-value	n
leukemia	2.21e-16	39
hematologic cancer	1.94e-15	51
immune system cancer	1.94e-15	51
myeloid leukemia	7.30e-14	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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191012285029429
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115722131597509
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327425836920237
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438774683880796
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324077625260234
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322268782634413
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464676368845168
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256329160216595
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764951456522548
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00901411467186345
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154752262882584
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00389290956253132
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109123736164574
HSF1#3297	3	164.290666666667	2.24910326529255e-07	1.19235581687253e-05
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128668202982973
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722996179991452
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246572400599366
PPARGC1A#10891	3	350.051136363636	2.31814761783079e-08	1.63695077118749e-06
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027811794429578
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247754372521562
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00645217466138276
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331049211236196
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140833465054673

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.