Coexpression cluster:C4046

Full id: C4046_breast_Mast_MCF7_lymphoma_CD19_migratory_lung

Phase1 CAGE Peaks

Hg19::chr20:46130602..46130613,+	p3@NCOA3
Hg19::chr20:46130619..46130664,+	p1@NCOA3
Hg19::chr20:46130672..46130686,+	p2@NCOA3

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><br>

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Cell Type

Ontology term	p-value	n
leukocyte	1.72e-36	140
nongranular leukocyte	5.72e-28	119
hematopoietic lineage restricted progenitor cell	1.04e-27	124
hematopoietic stem cell	9.18e-22	172
angioblastic mesenchymal cell	9.18e-22	172
hematopoietic oligopotent progenitor cell	3.17e-20	165
hematopoietic multipotent progenitor cell	3.17e-20	165
myeloid leukocyte	4.77e-20	76
CD14-positive, CD16-negative classical monocyte	1.24e-19	42
classical monocyte	1.69e-18	45
granulocyte monocyte progenitor cell	4.43e-18	71
hematopoietic cell	1.78e-17	182
macrophage dendritic cell progenitor	5.07e-16	65
myeloid lineage restricted progenitor cell	7.36e-16	70
monopoietic cell	1.55e-15	63
monocyte	1.55e-15	63
monoblast	1.55e-15	63
promonocyte	1.55e-15	63
lymphocyte of B lineage	3.48e-12	24
pro-B cell	3.48e-12	24
lymphoid lineage restricted progenitor cell	2.51e-11	52
lymphocyte	2.68e-11	53
common lymphoid progenitor	2.68e-11	53
myeloid cell	8.32e-10	112
common myeloid progenitor	8.32e-10	112
mesenchymal cell	2.92e-09	358
B cell	6.05e-09	14
connective tissue cell	2.71e-08	365

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.78e-17	102
blood island	1.78e-17	102
hemolymphoid system	9.08e-16	112
bone element	1.31e-14	86
bone marrow	5.98e-14	80
immune system	2.18e-12	115
skeletal element	1.50e-11	101
skeletal system	1.50e-11	101
connective tissue	4.67e-08	375

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	0.00129729769886249
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139300030952736
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190312736074011
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115372459217325
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661110440382441
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.000129973298232874
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279870882388036
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171994766473564
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325904274057806
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322825090226045
EBF1#1879	3	8.906466846569	0.0014152328356098	0.0091594163796401
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321149452129843
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463022150239023
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255898987512225
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167682063560761
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763303852927695
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243340041473864
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154340451486444
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00437307997145565
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434610499508984
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00391718278840296
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108849946782624
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122913632563054
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000757521737731939
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128280966257169
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157004823224017
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186836317681738
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00195107512316113
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720973053907664
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294939825833935
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269927107342236
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309229477722152
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173138131684847
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00883162964164563
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00664920822999928
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277230023112563
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239915267535119
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309461718892024
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246919744762706
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054391710728043
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629992839945373
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00614591361487815
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190604883654585
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329835442569162
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.01404345886774
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389601769837904

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.