Coexpression cluster:C1342

Full id: C1342_CD14_CD19_Eosinophils_Neutrophils_Peripheral_Natural_Basophils

Phase1 CAGE Peaks

Hg19::chr11:58346281..58346294,-	p@chr11:58346281..58346294 -
Hg19::chr1:155108603..155108650,-	p@chr1:155108603..155108650 -
Hg19::chr1:65532746..65532757,+	p@chr1:65532746..65532757 +
Hg19::chr5:137879399..137879412,-	p4@ETF1
Hg19::chr9:102581879..102581894,+	p@chr9:102581879..102581894 +
Hg19::chrX:24167676..24167700,-	p3@ZFX-AS1

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:0016149	translation release factor activity, codon specific	0.00120687625103026
GO:0006449	regulation of translational termination	0.00241375250206052
GO:0043022	ribosome binding	0.00261489854389889
GO:0008079	translation termination factor activity	0.00261489854389889
GO:0006415	translational termination	0.00261489854389889
GO:0003747	translation release factor activity	0.00261489854389889
GO:0043021	ribonucleoprotein binding	0.00293098518107349
GO:0043624	cellular protein complex disassembly	0.00337925350288473
GO:0043241	protein complex disassembly	0.00337925350288473
GO:0032984	macromolecular complex disassembly	0.00337925350288473
GO:0022411	cellular component disassembly	0.0053760851182257
GO:0006417	regulation of translation	0.0173272947469344
GO:0031326	regulation of cellular biosynthetic process	0.0173272947469344
GO:0008135	translation factor activity, nucleic acid binding	0.0173272947469344
GO:0009889	regulation of biosynthetic process	0.0174594764315711
GO:0051246	regulation of protein metabolic process	0.0318313611209231

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
leukocyte	6.36e-59	136
hematopoietic stem cell	3.53e-49	168
angioblastic mesenchymal cell	3.53e-49	168
hematopoietic lineage restricted progenitor cell	3.73e-48	120
nongranular leukocyte	6.76e-47	115
hematopoietic cell	4.11e-46	177
hematopoietic oligopotent progenitor cell	4.79e-45	161
hematopoietic multipotent progenitor cell	4.79e-45	161
classical monocyte	4.24e-44	42
CD14-positive, CD16-negative classical monocyte	4.24e-44	42
myeloid leukocyte	2.69e-39	72
defensive cell	1.47e-36	48
phagocyte	1.47e-36	48
granulocyte monocyte progenitor cell	2.12e-33	67
macrophage dendritic cell progenitor	2.62e-31	61
myeloid lineage restricted progenitor cell	1.21e-30	66
monopoietic cell	2.78e-29	59
monocyte	2.78e-29	59
monoblast	2.78e-29	59
promonocyte	2.78e-29	59
myeloid cell	1.28e-28	108
common myeloid progenitor	1.28e-28	108
stuff accumulating cell	5.66e-18	87
mesenchymal cell	2.72e-17	354
connective tissue cell	2.61e-16	361
motile cell	2.74e-16	386
lymphoid lineage restricted progenitor cell	5.20e-15	52
lymphocyte	1.56e-14	53
common lymphoid progenitor	1.56e-14	53
nucleate cell	1.24e-13	55
intermediate monocyte	2.78e-12	9
CD14-positive, CD16-positive monocyte	2.78e-12	9
stem cell	5.49e-12	441
multi fate stem cell	6.12e-12	427
somatic stem cell	9.72e-12	433
granulocyte	9.98e-09	8
lymphocyte of B lineage	1.31e-08	24
pro-B cell	1.31e-08	24
CD4-positive, alpha-beta T cell	9.48e-08	6
B cell	2.35e-07	14

Uber Anatomy

Ontology term	p-value	n
bone marrow	5.39e-29	76
bone element	3.81e-28	82
hematopoietic system	1.37e-26	98
blood island	1.37e-26	98
skeletal element	4.80e-24	90
immune system	1.27e-22	93
hemolymphoid system	2.42e-22	108
skeletal system	7.82e-21	100
connective tissue	1.39e-16	371
musculoskeletal system	4.28e-08	167
lateral plate mesoderm	1.77e-07	203

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
BCL3#602	2	11.5157009345794	0.0116272534680164	0.0424742471124925
E2F1#1869	5	4.08949101239944	0.00174981759776199	0.0107562801702569
E2F6#1876	5	4.18096310974782	0.00157359875958697	0.00997300084061553
NFKB1#4790	4	3.65870894946256	0.0120792728901523	0.0438219807341467
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0379956973831496
SIN3A#25942	5	4.50740393901261	0.00109611006120864	0.0076583247713787
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572685386474552
TBP#6908	5	3.08897557258032	0.00664544827578693	0.0282821504676003
ZNF263#10127	4	5.48122775800712	0.00267560938060723	0.0147421771617641

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.