Coexpression cluster:C3704

Full id: C3704_Eosinophils_Basophils_Mast_CD14_mature_immature_Neutrophils

Phase1 CAGE Peaks

Hg19::chr17:8339189..8339285,+	p1@NDEL1
Hg19::chr19:39897478..39897493,+	p1@ZFP36
Hg19::chr8:103667935..103667960,-	p1@KLF10

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:0000289	poly(A) tail shortening	0.00339482700640546
GO:0017091	AU-rich element binding	0.00339482700640546
GO:0050779	RNA destabilization	0.00339482700640546
GO:0048731	system development	0.00339482700640546
GO:0048856	anatomical structure development	0.00529648511130244
GO:0007275	multicellular organismal development	0.00650898764464172
GO:0000288	mRNA catabolic process, deadenylation-dependent decay	0.00650898764464172
GO:0043487	regulation of RNA stability	0.00931831515612074
GO:0043488	regulation of mRNA stability	0.00931831515612074
GO:0031348	negative regulation of defense response	0.00931831515612074
GO:0050728	negative regulation of inflammatory response	0.00931831515612074
GO:0032502	developmental process	0.0102721473776894
GO:0031124	mRNA 3'-end processing	0.0122633274630083
GO:0032501	multicellular organismal process	0.0126504045457779
GO:0045638	negative regulation of myeloid cell differentiation	0.0126504045457779
GO:0031123	RNA 3'-end processing	0.0126504045457779
GO:0051252	regulation of RNA metabolic process	0.0126504045457779
GO:0003727	single-stranded RNA binding	0.0126504045457779
GO:0031347	regulation of defense response	0.0142296101213018
GO:0050727	regulation of inflammatory response	0.0142296101213018
GO:0006402	mRNA catabolic process	0.0157184797707154
GO:0045637	regulation of myeloid cell differentiation	0.016401392162261
GO:0003729	mRNA binding	0.016401392162261
GO:0048583	regulation of response to stimulus	0.016401392162261
GO:0048523	negative regulation of cellular process	0.016401392162261
GO:0048513	organ development	0.016401392162261
GO:0048519	negative regulation of biological process	0.0169359510998705
GO:0006401	RNA catabolic process	0.0186902118941852
GO:0007179	transforming growth factor beta receptor signaling pathway	0.0196126044726536
GO:0045596	negative regulation of cell differentiation	0.0246356198112062
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.026074786722757
GO:0030099	myeloid cell differentiation	0.026074786722757
GO:0051093	negative regulation of developmental process	0.026074786722757
GO:0005819	spindle	0.026074786722757
GO:0048869	cellular developmental process	0.0294175409287247
GO:0030154	cell differentiation	0.0294175409287247
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0385264091806844
GO:0005813	centrosome	0.0385264091806844
GO:0045595	regulation of cell differentiation	0.0416849547241876
GO:0005815	microtubule organizing center	0.0416849547241876
GO:0030097	hemopoiesis	0.0445230348524182
GO:0048534	hemopoietic or lymphoid organ development	0.0466859166721047
GO:0002520	immune system development	0.0479597324192457

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
CD14-positive, CD16-negative classical monocyte	7.77e-25	42
myeloid leukocyte	8.66e-22	76
classical monocyte	4.46e-21	45
leukocyte	9.79e-21	140
granulocyte monocyte progenitor cell	1.28e-18	71
myeloid lineage restricted progenitor cell	1.65e-16	70
macrophage dendritic cell progenitor	3.65e-16	65
monopoietic cell	4.89e-15	63
monocyte	4.89e-15	63
monoblast	4.89e-15	63
promonocyte	4.89e-15	63
hematopoietic lineage restricted progenitor cell	2.15e-14	124
nongranular leukocyte	8.47e-13	119
hematopoietic stem cell	5.71e-09	172
angioblastic mesenchymal cell	5.71e-09	172
myeloid cell	5.58e-08	112
common myeloid progenitor	5.58e-08	112
hematopoietic cell	7.51e-08	182
hematopoietic oligopotent progenitor cell	1.10e-07	165
hematopoietic multipotent progenitor cell	1.10e-07	165
granulocyte	8.44e-07	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.34e-21	102
blood island	3.34e-21	102
hemolymphoid system	2.29e-19	112
bone marrow	4.50e-18	80
bone element	4.80e-16	86
skeletal element	1.15e-14	101
skeletal system	1.15e-14	101
immune system	3.46e-14	115
adult organism	2.82e-12	115
musculoskeletal system	2.67e-07	167

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	0.0189881407486239
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321882626942006
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320403474574536
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108633138898639
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269420634305005
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460390953256262
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276463520597988
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054243918640823
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329059851613583

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.