Coexpression cluster:C4473

Full id: C4473_Neutrophils_CD14_Eosinophils_lymphangiectasia_Dendritic_myeloma_Burkitt

Phase1 CAGE Peaks

Hg19::chr5:142782862..142782881,-	p11@NR3C1
Hg19::chr6:90062427..90062459,-	p1@UBE2J1
Hg19::chr6:90062488..90062504,-	p3@UBE2J1

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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GO ID	GO name	FDR corrected p-value
GO:0004883	glucocorticoid receptor activity	0.0057694572000471

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	5.61e-36	140
myeloid leukocyte	3.13e-31	76
nongranular leukocyte	2.05e-30	119
hematopoietic lineage restricted progenitor cell	4.03e-28	124
granulocyte monocyte progenitor cell	1.84e-27	71
hematopoietic stem cell	2.61e-27	172
angioblastic mesenchymal cell	2.61e-27	172
macrophage dendritic cell progenitor	1.69e-26	65
hematopoietic cell	6.54e-26	182
CD14-positive, CD16-negative classical monocyte	1.47e-25	42
monopoietic cell	1.48e-25	63
monocyte	1.48e-25	63
monoblast	1.48e-25	63
promonocyte	1.48e-25	63
hematopoietic oligopotent progenitor cell	4.68e-24	165
hematopoietic multipotent progenitor cell	4.68e-24	165
myeloid lineage restricted progenitor cell	1.42e-23	70
classical monocyte	3.50e-21	45
myeloid cell	4.53e-18	112
common myeloid progenitor	4.53e-18	112
mesenchymal cell	1.21e-15	358
connective tissue cell	8.41e-15	365
multi fate stem cell	1.09e-13	430
somatic stem cell	6.61e-12	436
lymphocyte of B lineage	6.89e-12	24
pro-B cell	6.89e-12	24
stem cell	4.24e-11	444
motile cell	1.78e-09	390
B cell	2.69e-08	14
granulocyte	8.38e-07	8
intermediate monocyte	9.35e-07	9
CD14-positive, CD16-positive monocyte	9.35e-07	9

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	6.10e-30	112
hematopoietic system	2.35e-29	102
blood island	2.35e-29	102
lateral plate mesoderm	3.68e-25	216
bone marrow	2.92e-24	80
immune system	1.44e-23	115
bone element	1.07e-22	86
skeletal element	6.10e-19	101
skeletal system	6.10e-19	101
connective tissue	1.56e-14	375
musculoskeletal system	3.77e-13	167
mesoderm	3.09e-08	448
mesoderm-derived structure	3.09e-08	448
presumptive mesoderm	3.09e-08	448

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	0.0190834698301064
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280832956657583
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306936077166341
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327086485297725
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323849169191671
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464373273956635
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.0038911009258641
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155877568258534
THAP1#55145	2	20.9127630685675	0.00298344741373694	0.0158763000327765
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330813191160643

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.