Coexpression cluster:C4335

Full id: C4335_Mast_Basophils_immature_CD14_Eosinophils_serous_CD8

Phase1 CAGE Peaks

Hg19::chr3:5021113..5021180,+	p1@BHLHE40
Hg19::chr3:5021191..5021202,+	p3@BHLHE40
Hg19::chr3:5022254..5022271,+	p12@BHLHE40

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 leukocyte	2.07e-17	76
CD14-positive, CD16-negative classical monocyte	5.49e-17	42
classical monocyte	1.90e-15	45
granulocyte monocyte progenitor cell	5.21e-15	71
myeloid lineage restricted progenitor cell	7.27e-13	70
macrophage dendritic cell progenitor	9.43e-13	65
leukocyte	7.98e-12	140
monopoietic cell	1.05e-11	63
monocyte	1.05e-11	63
monoblast	1.05e-11	63
promonocyte	1.05e-11	63
myeloid cell	3.71e-09	112
common myeloid progenitor	3.71e-09	112
hematopoietic lineage restricted progenitor cell	5.15e-07	124

Uber Anatomy

Ontology term	p-value	n
bone marrow	5.21e-13	80
hematopoietic system	2.49e-12	102
blood island	2.49e-12	102
bone element	7.12e-12	86
hemolymphoid system	2.94e-10	112
immune system	1.21e-09	115
lateral plate mesoderm	3.16e-09	216
skeletal element	2.82e-08	101
skeletal system	2.82e-08	101
organ	6.02e-07	511

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.025965902915649
BHLHE40#8553	2	29.9145423646516	0.00146748352710614	0.00939914829433575
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323519745154153
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321738897438127
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016798389127517
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00900166110976969
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128484854672244
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309691289964867
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173419629361627
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.0088423586034865
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165693210758651
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247385140967878
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00630725070472696
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330503150681579
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109761858010383

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.