Coexpression cluster:C1590

Full id: C1590_Mast_CD19_Basophils_CD4_Natural_Eosinophils_CD8

Phase1 CAGE Peaks

Hg19::chr10:63806474..63806496,+	p@chr10:63806474..63806496 +
Hg19::chr11:73694239..73694253,-	p2@UCP2
Hg19::chr11:73694257..73694289,-	p3@UCP2
Hg19::chr12:25539261..25539297,+	p@chr12:25539261..25539297 +
Hg19::chr22:32188667..32188693,+	p2@DEPDC5

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:0000303	response to superoxide	0.00735856827869091
GO:0000305	response to oxygen radical	0.00735856827869091
GO:0000302	response to reactive oxygen species	0.0264822674140548
GO:0006839	mitochondrial transport	0.0352987719354742
GO:0007005	mitochondrion organization and biogenesis	0.0495752912277362
GO:0006979	response to oxidative stress	0.0495752912277362
GO:0015992	proton transport	0.0495752912277362
GO:0006818	hydrogen transport	0.0495752912277362

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	9.68e-73	172
angioblastic mesenchymal cell	9.68e-73	172
hematopoietic cell	4.54e-70	182
hematopoietic oligopotent progenitor cell	1.52e-68	165
hematopoietic multipotent progenitor cell	1.52e-68	165
leukocyte	1.69e-61	140
hematopoietic lineage restricted progenitor cell	3.38e-52	124
nongranular leukocyte	2.57e-49	119
myeloid cell	2.14e-40	112
common myeloid progenitor	2.14e-40	112
myeloid leukocyte	4.38e-30	76
granulocyte monocyte progenitor cell	1.01e-26	71
myeloid lineage restricted progenitor cell	3.95e-26	70
lymphocyte	3.21e-24	53
common lymphoid progenitor	3.21e-24	53
lymphoid lineage restricted progenitor cell	1.11e-23	52
macrophage dendritic cell progenitor	5.99e-23	65
monopoietic cell	3.46e-22	63
monocyte	3.46e-22	63
monoblast	3.46e-22	63
promonocyte	3.46e-22	63
classical monocyte	7.39e-18	45
CD14-positive, CD16-negative classical monocyte	9.62e-18	42
mesenchymal cell	1.24e-13	358
connective tissue cell	8.67e-13	365
lymphocyte of B lineage	1.14e-12	24
pro-B cell	1.14e-12	24
motile cell	2.87e-11	390
mature alpha-beta T cell	1.59e-10	18
alpha-beta T cell	1.59e-10	18
immature T cell	1.59e-10	18
mature T cell	1.59e-10	18
immature alpha-beta T cell	1.59e-10	18
T cell	1.91e-10	25
pro-T cell	1.91e-10	25
B cell	4.74e-10	14
CD8-positive, alpha-beta T cell	9.54e-07	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.09e-31	102
blood island	1.09e-31	102
hemolymphoid system	3.47e-27	112
bone marrow	1.32e-21	80
bone element	1.64e-18	86
immune system	8.57e-16	115
connective tissue	3.27e-12	375
skeletal element	5.22e-12	101
skeletal system	5.22e-12	101
blood	2.00e-08	15
haemolymphatic fluid	2.00e-08	15
organism substance	2.00e-08	15

Disease

Ontology term	p-value	n
hematologic cancer	1.05e-12	51
immune system cancer	1.05e-12	51
leukemia	3.97e-10	39
myeloid leukemia	5.61e-09	31

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	26.9230881281864	0.000106941952374384	0.00148918807520377
E2F4#1874	3	7.60083618917066	0.00435414736037571	0.0206466649793543
EBF1#1879	4	7.1251734772552	0.000723053104677421	0.00576890322378955
GTF2B#2959	2	12.7775319737297	0.0091993608955972	0.0347828561499991
IRF3#3661	2	18.7927808845958	0.00433962977712151	0.0205843670766097
JUNB#3726	2	12.2442530639285	0.00999049059334596	0.037464877812512
NFYB#4801	3	10.0558759521219	0.00193816560672546	0.0113859870514569
POU2F2#5452	3	5.46367443464551	0.0111565009446978	0.040996931922286
RFX5#5993	3	7.22874649631706	0.0050291827895866	0.0234630046172445
SMARCB1#6598	3	10.9516294686944	0.00151187284834318	0.00964972733655892
SP2#6668	2	10.4614121975379	0.0135319118334714	0.0477726849871858
SREBF1#6720	2	18.8023397761953	0.00433531272958737	0.0205751034338533

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.