Coexpression cluster:C2428

Full id: C2428_Mast_CD14_Eosinophils_immature_CD19_CD4_CD8

Phase1 CAGE Peaks

Hg19::chr17:62502942..62502965,-	p6@DDX5
Hg19::chr2:157189180..157189290,-	p1@NR4A2
Hg19::chr2:157189298..157189305,-	p23@NR4A2
Hg19::chr9:102584128..102584144,+	p3@NR4A3

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:0003707	steroid hormone receptor activity	0.00364664345425225
GO:0004879	ligand-dependent nuclear receptor activity	0.00364664345425225
GO:0042053	regulation of dopamine metabolic process	0.0106843266182394
GO:0042069	regulation of catecholamine metabolic process	0.0106843266182394
GO:0004887	thyroid hormone receptor activity	0.0195838960000424
GO:0042417	dopamine metabolic process	0.0195838960000424
GO:0016070	RNA metabolic process	0.0284680595302614
GO:0043565	sequence-specific DNA binding	0.0284680595302614
GO:0006584	catecholamine metabolic process	0.0284680595302614
GO:0018958	phenol metabolic process	0.0284680595302614
GO:0003724	RNA helicase activity	0.0284680595302614
GO:0042133	neurotransmitter metabolic process	0.0284680595302614
GO:0010467	gene expression	0.038496700016013
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0428660141712666
GO:0003700	transcription factor activity	0.0428660141712666
GO:0005634	nucleus	0.0428660141712666
GO:0006576	biogenic amine metabolic process	0.0437664922796501
GO:0003676	nucleic acid binding	0.0437664922796501
GO:0001505	regulation of neurotransmitter levels	0.0437664922796501
GO:0065007	biological regulation	0.0456741439377732
GO:0006575	amino acid derivative metabolic process	0.0456741439377732

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 leukocyte	5.32e-25	72
classical monocyte	1.13e-24	42
CD14-positive, CD16-negative classical monocyte	1.13e-24	42
leukocyte	2.92e-24	136
defensive cell	1.55e-22	48
phagocyte	1.55e-22	48
granulocyte monocyte progenitor cell	6.83e-22	67
macrophage dendritic cell progenitor	1.46e-19	61
myeloid lineage restricted progenitor cell	8.04e-19	66
hematopoietic stem cell	2.36e-18	168
angioblastic mesenchymal cell	2.36e-18	168
monopoietic cell	2.41e-18	59
monocyte	2.41e-18	59
monoblast	2.41e-18	59
promonocyte	2.41e-18	59
hematopoietic lineage restricted progenitor cell	1.12e-17	120
nongranular leukocyte	9.99e-17	115
myeloid cell	1.86e-16	108
common myeloid progenitor	1.86e-16	108
hematopoietic oligopotent progenitor cell	3.47e-16	161
hematopoietic multipotent progenitor cell	3.47e-16	161
hematopoietic cell	8.28e-16	177
stuff accumulating cell	5.49e-08	87

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.54e-17	76
bone element	3.44e-17	82
hematopoietic system	1.14e-15	98
blood island	1.14e-15	98
skeletal element	9.33e-14	90
skeletal system	6.82e-13	100
immune system	1.55e-12	93
hemolymphoid system	1.10e-11	108
adult organism	8.80e-11	114

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
BRCA1#672	3	15.1381729824178	0.000468218442143119	0.00430119323414418
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00512049970145601
CTBP2#1488	2	31.3585001696641	0.00149267688204723	0.00954003309981829
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.010647851625104
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109271630570403
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.0099665597993063
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160845556010242
ELK4#2005	3	12.176761243851	0.000891263257762061	0.00663738187231973
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0192041943348221
FOXA1#3169	4	11.0814197493855	6.62943068949433e-05	0.00107029078958123
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378577383842944
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185959014019722
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307392060598514
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466190361441652
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00887417539554322
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508707670121959
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.0061886734861336
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123846185380533
SETDB1#9869	2	20.1600130890052	0.0035690868540764	0.0180842160854301
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795946997031712
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00683851605342781
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322061413795887
TBP#6908	4	3.70677068709639	0.00529637781478435	0.024408631303427
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115400038481509
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00507846503795197
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106814179676716

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.