Coexpression cluster:C2375

Full id: C2375_Whole_chronic_Neutrophils_blood_Reticulocytes_liver_acute

Phase1 CAGE Peaks

Hg19::chr16:47496118..47496129,+	p@chr16:47496118..47496129 +
Hg19::chr17:40472067..40472092,-	p@chr17:40472067..40472092 -
Hg19::chr17:60759119..60759136,+	p8@MRC2
Hg19::chr1:150949632..150949662,-	p@chr1:150949632..150949662 -

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
histamine secreting cell	8.51e-19	5
biogenic amine secreting cell	8.51e-19	5
granulocytopoietic cell	8.51e-19	5
mast cell	8.51e-19	5
mast cell progenitor	8.51e-19	5
basophil mast progenitor cell	8.51e-19	5
myeloid cell	3.34e-12	108
common myeloid progenitor	3.34e-12	108
basophil	4.22e-12	3
endocrine cell	2.45e-10	9
erythroid lineage cell	2.72e-09	2
erythroblast	2.72e-09	2
megakaryocyte-erythroid progenitor cell	2.72e-09	2
erythroid progenitor cell	2.72e-09	2
reticulocyte	2.72e-09	2
proerythroblast	2.72e-09	2
basophilic erythroblast	2.72e-09	2
polychromatophilic erythroblast	2.72e-09	2
orthochromatic erythroblast	2.72e-09	2
granulocyte	5.90e-08	8
hematopoietic stem cell	1.05e-07	168
angioblastic mesenchymal cell	1.05e-07	168
hematopoietic cell	4.78e-07	177

Uber Anatomy

Ontology term	p-value	n
blood	1.35e-31	15
haemolymphatic fluid	1.35e-31	15
organism substance	1.35e-31	15
hematopoietic system	1.71e-12	98
blood island	1.71e-12	98
hemolymphoid system	6.82e-11	108
hemopoietic organ	1.07e-08	7
immune organ	1.07e-08	7

Disease

Ontology term	p-value	n
chronic leukemia	1.55e-18	8
myeloid leukemia	2.62e-11	31
leukemia	1.40e-08	39

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
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418846182179885
FOSL1#8061	2	19.8567898581865	0.00367705000923323	0.0185592222073415
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378523187159383
GATA1#2623	4	13.5603081438004	2.95627390049268e-05	0.000613817673744642
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000721390500969013
GTF2B#2959	2	15.9719149671621	0.00563658572353722	0.025471826246398
HDAC8#55869	1	194.146008403361	0.00514086390100343	0.0239018245540176
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185853205192399
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0282907493742505
JUNB#3726	2	15.3053163299106	0.00612694714847562	0.0270980025933618
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0386806776558596
MAFK#7975	2	13.550366568915	0.0077720281209805	0.0319542888326542
POLR3A#11128	1	84.7830275229358	0.0117428417771162	0.0428620086100805
REST#5978	4	9.65002871612802	0.000115282561421917	0.00156872904655943
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321875437463621
TAL1#6886	4	29.8686166774402	1.25525650806991e-06	5.03640931411114e-05
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243924858931191

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.