Coexpression cluster:C1356

Full id: C1356_CD14_thymus_Hodgkin_NK_anaplastic_hepatoblastoma_lymphangiectasia

Phase1 CAGE Peaks

Hg19::chr12:123717458..123717464,+	p2@C12orf65
Hg19::chr12:58241001..58241005,+	p@chr12:58241001..58241005 +
Hg19::chr14:99947613..99947617,-	p8@SETD3
Hg19::chr19:56116608..56116632,-	p@chr19:56116608..56116632 -
Hg19::chr1:147071419..147071423,-	p@chr1:147071419..147071423 -
Hg19::chr4:100871681..100871699,+	p1@ENST00000501976

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:0008079	translation termination factor activity	0.00739694285085992
GO:0006415	translational termination	0.00739694285085992
GO:0003747	translation release factor activity	0.00739694285085992
GO:0043624	cellular protein complex disassembly	0.00796417945172759
GO:0043241	protein complex disassembly	0.00796417945172759
GO:0032984	macromolecular complex disassembly	0.00796417945172759
GO:0022411	cellular component disassembly	0.0119425752711976
GO:0008135	translation factor activity, nucleic acid binding	0.0427693486322997

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	7.51e-17	168
angioblastic mesenchymal cell	7.51e-17	168
hematopoietic cell	1.39e-16	177
classical monocyte	4.86e-16	42
CD14-positive, CD16-negative classical monocyte	4.86e-16	42
hematopoietic oligopotent progenitor cell	1.12e-15	161
hematopoietic multipotent progenitor cell	1.12e-15	161
leukocyte	5.78e-14	136
nongranular leukocyte	2.01e-13	115
hematopoietic lineage restricted progenitor cell	2.93e-13	120
defensive cell	2.97e-12	48
phagocyte	2.97e-12	48
myeloid cell	1.35e-11	108
common myeloid progenitor	1.35e-11	108
macrophage dendritic cell progenitor	1.42e-10	61
granulocyte monocyte progenitor cell	1.45e-10	67
monopoietic cell	5.83e-10	59
monocyte	5.83e-10	59
monoblast	5.83e-10	59
promonocyte	5.83e-10	59
myeloid lineage restricted progenitor cell	1.34e-09	66
myeloid leukocyte	4.05e-08	72

Uber Anatomy

Ontology term	p-value	n
bone element	2.86e-09	82
bone marrow	6.61e-09	76
hematopoietic system	9.85e-09	98
blood island	9.85e-09	98
immune system	7.35e-08	93
skeletal element	3.96e-07	90
hemolymphoid system	9.42e-07	108

Disease

Ontology term	p-value	n
cancer	8.47e-18	235
disease of cellular proliferation	1.44e-16	239
cell type cancer	6.03e-12	143
carcinoma	3.30e-11	106
hematologic cancer	2.02e-08	51
immune system cancer	2.02e-08	51
organ system cancer	2.12e-07	137

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	0.0424757327974452
BHLHE40#8553	2	14.9572711823258	0.0070165594845194	0.029638117533012
CCNT2#905	5	5.28016798080219	0.000510094397483253	0.0044666511929868
CHD2#1106	4	6.89601522274457	0.00111539132013599	0.00765980760676503
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.0101306256951669
GTF2B#2959	2	10.6479433114414	0.0135134586576011	0.0477236705353264
HEY1#23462	5	3.36675920258809	0.00442382704520303	0.0209475912574338
HMGN3#9324	4	5.45236514890039	0.00272961688233377	0.0149852006714706
IRF1#3659	5	6.36430312796992	0.00020566751420509	0.00243893601862898
IRF3#3661	2	15.6606507371632	0.00641762098993253	0.0279131233786258
NFYA#4800	3	9.21279034991526	0.00282275556436427	0.0154494166432575
NFYB#4801	3	8.37989662676823	0.00370399687862904	0.0186825910367593
PAX5#5079	4	4.44637702078522	0.00587473351924079	0.0263598253143147
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.038003833797165
POU2F2#5452	4	6.07074937182835	0.00181532620952452	0.0108928959492405
RDBP#7936	2	51.2128013300083	0.000624018049350717	0.00513730262148349
SIN3A#25942	4	3.60592315121009	0.0127389384448714	0.0459390902332074
SP1#6667	6	5.6983813781409	2.91961319085282e-05	0.000609112029643384
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572773087146294
TAF7#6879	4	7.62204626994928	0.00075927901514148	0.00596586977598262
TBP#6908	6	3.70677068709639	0.00038541647290796	0.0037756787368947
ZBTB7A#51341	4	4.90127287191726	0.00407962811884375	0.0194829338837589

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.