Coexpression cluster:C3956

Full id: C3956_Mast_cord_Hodgkin_granulocyte_rhabdomyosarcoma_lymphoma_acute

Phase1 CAGE Peaks

Hg19::chr1:24306768..24306779,-	p3@SRSF10
Hg19::chr1:24306809..24306828,-	p1@SRSF10
Hg19::chr1:24306835..24306868,-	p2@SRSF10

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
hematopoietic stem cell	4.85e-34	168
angioblastic mesenchymal cell	4.85e-34	168
hematopoietic cell	1.02e-31	177
hematopoietic oligopotent progenitor cell	9.01e-31	161
hematopoietic multipotent progenitor cell	9.01e-31	161
nucleate cell	1.83e-24	55
lymphocyte	2.39e-23	53
common lymphoid progenitor	2.39e-23	53
lymphoid lineage restricted progenitor cell	1.01e-22	52
leukocyte	2.23e-21	136
hematopoietic lineage restricted progenitor cell	1.45e-19	120
nongranular leukocyte	7.19e-19	115
lymphocyte of B lineage	2.74e-11	24
pro-B cell	2.74e-11	24
T cell	2.92e-11	25
pro-T cell	2.92e-11	25
myeloid cell	9.68e-11	108
common myeloid progenitor	9.68e-11	108
motile cell	1.94e-09	386
mature alpha-beta T cell	8.33e-09	18
alpha-beta T cell	8.33e-09	18
immature T cell	8.33e-09	18
mature T cell	8.33e-09	18
immature alpha-beta T cell	8.33e-09	18
mesenchymal cell	4.23e-08	354
B cell	7.90e-08	14

Uber Anatomy

Ontology term	p-value	n
connective tissue	1.59e-07	371

Disease

Ontology term	p-value	n
cancer	2.47e-27	235
disease of cellular proliferation	2.44e-25	239
hematologic cancer	2.23e-19	51
immune system cancer	2.23e-19	51
organ system cancer	3.21e-18	137
leukemia	5.04e-16	39
cell type cancer	7.06e-12	143
myeloid leukemia	7.50e-12	31
carcinoma	3.05e-11	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
BCL3#602	2	23.0314018691589	0.00246467476084291	0.0138547912884263
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164273515204955
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.019018048873587
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.011528214809465
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660740044449739
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279674643782113
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171863971974345
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032561605449198
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437503956516916
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322510323172392
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320880010899317
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462689553517456
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762841742428816
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000628302740861917
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434311489877399
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108781713968936
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128175760434651
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00444524612248821
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186710677235629
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00195059509483706
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720727105536952
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294761979822217
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000738050292877498
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269788789582901
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245998086001697
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471397923561907
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173035995337378
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00882881055659659
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00664544949159906
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000359028924275861
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277043814289684
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203237899238246
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246747020768643
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.010912773667408
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375303565259649
STAT2#6773	3	65.2637711864407	3.59360517547754e-06	0.000118395120164574
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543494023033946
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000720136706194579
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197189512724237
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190425928736122
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329699758580072
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000633996463630228
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.010951873894974

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.