Coexpression cluster:C1121

Full id: C1121_Hodgkin_CD4_acute_CD8_thymus_Natural_chronic

Phase1 CAGE Peaks

Hg19::chr10:73975408..73975422,+	p5@ANAPC16
Hg19::chr2:240220167..240220189,-	p11@HDAC4
Hg19::chr2:240220194..240220214,-	p9@HDAC4
Hg19::chr2:240220219..240220235,-	p8@HDAC4
Hg19::chr2:98330032..98330054,+	p1@ZAP70
Hg19::chr5:133485552..133485556,+	p@chr5:133485552..133485556 +
Hg19::chr7:142511881..142511883,+	p@chr7:142511881..142511883 +

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:0030098	lymphocyte differentiation	0.000537903997551219
GO:0002521	leukocyte differentiation	0.000537903997551219
GO:0046649	lymphocyte activation	0.000632053985636964
GO:0030097	hemopoiesis	0.000632053985636964
GO:0048534	hemopoietic or lymphoid organ development	0.000632053985636964
GO:0045321	leukocyte activation	0.000632053985636964
GO:0002520	immune system development	0.000632053985636964
GO:0001775	cell activation	0.000729830292807322
GO:0045059	positive thymic T cell selection	0.00182500551798389
GO:0043368	positive T cell selection	0.00182500551798389
GO:0045582	positive regulation of T cell differentiation	0.00331809417225125
GO:0045061	thymic T cell selection	0.0038019269439903
GO:0045621	positive regulation of lymphocyte differentiation	0.00491311479580289
GO:0045843	negative regulation of striated muscle development	0.00513229918112986
GO:0045058	T cell selection	0.00513229918112986
GO:0033077	T cell differentiation in the thymus	0.00513229918112986
GO:0045580	regulation of T cell differentiation	0.00536703125000323
GO:0042101	T cell receptor complex	0.00608245633918467
GO:0016202	regulation of striated muscle development	0.00624242908466399
GO:0045619	regulation of lymphocyte differentiation	0.007298517821056
GO:0001772	immunological synapse	0.00738529621235706
GO:0048513	organ development	0.00794090620559271
GO:0000118	histone deacetylase complex	0.00912220711952032
GO:0002376	immune system process	0.0105808254741684
GO:0030183	B cell differentiation	0.0105808254741684
GO:0004407	histone deacetylase activity	0.0119695475357714
GO:0048731	system development	0.0119695475357714
GO:0033558	protein deacetylase activity	0.0119695475357714
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0119695475357714
GO:0050870	positive regulation of T cell activation	0.0119695475357714
GO:0030217	T cell differentiation	0.0119695475357714
GO:0019213	deacetylase activity	0.0119695475357714
GO:0048869	cellular developmental process	0.0129342269232722
GO:0030154	cell differentiation	0.0129342269232722
GO:0051251	positive regulation of lymphocyte activation	0.0132868791745255
GO:0050863	regulation of T cell activation	0.0145852078161808
GO:0048856	anatomical structure development	0.0145852078161808
GO:0042113	B cell activation	0.0146353502126821
GO:0051249	regulation of lymphocyte activation	0.0177390866745995
GO:0007275	multicellular organismal development	0.0177390866745995
GO:0050865	regulation of cell activation	0.0177844908429431
GO:0014706	striated muscle development	0.0188625001807961
GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	0.0188625001807961
GO:0042110	T cell activation	0.0202952075698475
GO:0043235	receptor complex	0.0222701656554202
GO:0043234	protein complex	0.0242595666410333
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0246116247363006
GO:0032502	developmental process	0.0313359353861005
GO:0007517	muscle development	0.0319505627797065
GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.033853171416462
GO:0045892	negative regulation of transcription, DNA-dependent	0.035282625829304
GO:0001501	skeletal development	0.035282625829304
GO:0005667	transcription factor complex	0.035282625829304
GO:0016564	transcription repressor activity	0.035282625829304
GO:0032501	multicellular organismal process	0.035282625829304
GO:0016568	chromatin modification	0.035282625829304
GO:0032991	macromolecular complex	0.035282625829304
GO:0008285	negative regulation of cell proliferation	0.035282625829304
GO:0051239	regulation of multicellular organismal process	0.0426678257933063
GO:0006954	inflammatory response	0.043345702468306
GO:0016481	negative regulation of transcription	0.043345702468306
GO:0004713	protein-tyrosine kinase activity	0.0449807666101281
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0459889232023415

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
T cell	5.98e-54	25
pro-T cell	5.98e-54	25
mature alpha-beta T cell	2.66e-43	18
alpha-beta T cell	2.66e-43	18
immature T cell	2.66e-43	18
mature T cell	2.66e-43	18
immature alpha-beta T cell	2.66e-43	18
lymphoid lineage restricted progenitor cell	1.53e-31	52
lymphocyte	8.67e-31	53
common lymphoid progenitor	8.67e-31	53
nucleate cell	2.29e-29	55
CD8-positive, alpha-beta T cell	8.63e-27	11
leukocyte	2.49e-21	136
nongranular leukocyte	2.79e-21	115
hematopoietic lineage restricted progenitor cell	5.46e-16	120
CD4-positive, alpha-beta T cell	7.13e-16	6
hematopoietic stem cell	3.72e-15	168
angioblastic mesenchymal cell	3.72e-15	168
hematopoietic cell	9.86e-15	177
hematopoietic oligopotent progenitor cell	4.04e-12	161
hematopoietic multipotent progenitor cell	4.04e-12	161
single nucleate cell	6.28e-09	3
mononuclear cell	6.28e-09	3
natural killer cell	9.74e-09	3
pro-NK cell	9.74e-09	3
naive T cell	3.11e-08	3
basophil	1.02e-07	3
circulating cell	3.60e-07	6

Uber Anatomy

Ontology term	p-value	n
blood	3.65e-18	15
haemolymphatic fluid	3.65e-18	15
organism substance	3.65e-18	15
hemopoietic organ	2.54e-12	7
immune organ	2.54e-12	7
thymus	8.96e-11	4
hemolymphoid system gland	8.96e-11	4
thymic region	8.96e-11	4
pharyngeal gland	8.96e-11	4
thymus primordium	8.96e-11	4
neck	2.57e-08	10
hemolymphoid system	3.86e-08	108
hematopoietic system	7.37e-08	98
blood island	7.37e-08	98
pharyngeal epithelium	3.72e-07	6

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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No analysis results for this cluster

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.