Coexpression cluster:C4732

Full id: C4732_Hepatocyte_Neutrophils_CD14_granulocyte_small_Eosinophils_duodenum

Phase1 CAGE Peaks

Hg19::chr8:144635648..144635661,-	p@chr8:144635648..144635661 -
Hg19::chr8:144635664..144635703,-	p@chr8:144635664..144635703 -
Hg19::chr8:144635740..144635767,-	p@chr8:144635740..144635767 -

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
myeloid cell	6.54e-24	112
common myeloid progenitor	6.54e-24	112
myeloid leukocyte	7.99e-24	76
granulocyte monocyte progenitor cell	1.81e-21	71
CD14-positive, CD16-negative classical monocyte	1.58e-20	42
myeloid lineage restricted progenitor cell	2.01e-20	70
macrophage dendritic cell progenitor	3.84e-20	65
monopoietic cell	7.65e-20	63
monocyte	7.65e-20	63
monoblast	7.65e-20	63
promonocyte	7.65e-20	63
classical monocyte	4.04e-19	45
hematopoietic stem cell	5.05e-19	172
angioblastic mesenchymal cell	5.05e-19	172
hematopoietic oligopotent progenitor cell	1.39e-18	165
hematopoietic multipotent progenitor cell	1.39e-18	165
leukocyte	8.71e-17	140
hematopoietic cell	1.04e-15	182
hematopoietic lineage restricted progenitor cell	2.25e-14	124
nongranular leukocyte	1.79e-13	119
connective tissue cell	5.31e-07	365
mesenchymal cell	5.92e-07	358

Uber Anatomy

Ontology term	p-value	n
immune system	3.35e-22	115
bone marrow	1.51e-21	80
hematopoietic system	2.50e-18	102
blood island	2.50e-18	102
hemolymphoid system	1.83e-17	112
bone element	3.21e-17	86
skeletal element	3.38e-14	101
skeletal system	3.38e-14	101
adult organism	1.44e-08	115
musculoskeletal system	2.38e-08	167
connective tissue	6.93e-07	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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191243642497554
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281427398460087
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465123756862762
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154865693860613
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123435291474854
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.00076040753482806
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128767145905183
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000606504434998874
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00310340149297329
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00166012917236832
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024796118826243
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109443536351919
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155408384499105
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00645867840141151
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00632148621778459
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331372732359749
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243881388567479

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.