Coexpression cluster:C4465

Full id: C4465_lymphoma_chronic_acute_granulocyte_merkel_carcinosarcoma_Burkitt

Phase1 CAGE Peaks

Hg19::chr5:134734814..134734819,-	p8@H2AFY
Hg19::chr5:134734827..134734836,-	p5@H2AFY
Hg19::chr5:134734841..134734864,-	p3@H2AFY

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	1.50e-20	172
angioblastic mesenchymal cell	1.50e-20	172
hematopoietic cell	2.13e-19	182
hematopoietic oligopotent progenitor cell	4.63e-19	165
hematopoietic multipotent progenitor cell	4.63e-19	165
leukocyte	1.10e-15	140
myeloid cell	4.87e-15	112
common myeloid progenitor	4.87e-15	112
hematopoietic lineage restricted progenitor cell	2.03e-14	124
nongranular leukocyte	2.65e-14	119
myeloid leukocyte	2.85e-12	76
macrophage dendritic cell progenitor	8.41e-12	65
granulocyte monocyte progenitor cell	3.76e-11	71
monopoietic cell	3.90e-11	63
monocyte	3.90e-11	63
monoblast	3.90e-11	63
promonocyte	3.90e-11	63
myeloid lineage restricted progenitor cell	8.08e-11	70

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.05e-11	102
blood island	7.05e-11	102
bone marrow	1.37e-10	80
bone element	1.15e-09	86
hemolymphoid system	3.49e-09	112
immune system	6.77e-08	115
skeletal element	2.86e-07	101
skeletal system	2.86e-07	101

Disease

Ontology term	p-value	n
cancer	7.69e-18	235
disease of cellular proliferation	5.04e-16	239
organ system cancer	2.44e-12	137
hematologic cancer	2.35e-11	51
immune system cancer	2.35e-11	51
carcinoma	7.26e-09	106
cell type cancer	7.38e-09	143
leukemia	9.21e-08	39

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
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000285500342615284
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190816957788068
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327074378606187
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438437597055791
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323823805065012
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00918274739800275
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322009783612778
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464341392231054
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.015465516850035
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109036472081275
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123290943816354
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295617602405155
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000606015811083468
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173496560388059
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00884858203074598
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165799642677175
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277895431202399
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203696022394674
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544807731783579
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.0061635886116321
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330788366517752
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140727881435161
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00390282641216392
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109896676927048

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.