Coexpression cluster:C792

Full id: C792_CD4_chronic_Whole_blood_CD19_biphenotypic_Natural

Phase1 CAGE Peaks

Hg19::chr11:118183437..118183448,-	p@chr11:118183437..118183448 -
Hg19::chr11:67203465..67203500,+	p@chr11:67203465..67203500 +
Hg19::chr16:68390556..68390581,+	p@chr16:68390556..68390581 +
Hg19::chr6:31548335..31548356,+	p@chr6:31548335..31548356 +
Hg19::chr6:31548428..31548469,+	p3@AK095821
Hg19::chr6:31548438..31548449,-	p@chr6:31548438..31548449 -
Hg19::chr6:31548476..31548492,-	p@chr6:31548476..31548492 -
Hg19::chr6:31548554..31548577,-	p@chr6:31548554..31548577 -
Hg19::chr6:31548595..31548608,-	p@chr6:31548595..31548608 -
Hg19::chr6:31549373..31549385,-	p@chr6:31549373..31549385 -

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
hematopoietic stem cell	2.00e-44	172
angioblastic mesenchymal cell	2.00e-44	172
lymphocyte	3.77e-42	53
common lymphoid progenitor	3.77e-42	53
hematopoietic cell	1.52e-41	182
lymphoid lineage restricted progenitor cell	1.86e-41	52
hematopoietic oligopotent progenitor cell	1.49e-39	165
hematopoietic multipotent progenitor cell	1.49e-39	165
leukocyte	2.13e-39	140
nongranular leukocyte	9.83e-34	119
hematopoietic lineage restricted progenitor cell	1.75e-30	124
T cell	9.14e-22	25
pro-T cell	9.14e-22	25
lymphocyte of B lineage	6.18e-18	24
pro-B cell	6.18e-18	24
mature alpha-beta T cell	4.00e-17	18
alpha-beta T cell	4.00e-17	18
immature T cell	4.00e-17	18
mature T cell	4.00e-17	18
immature alpha-beta T cell	4.00e-17	18
B cell	3.36e-13	14
CD8-positive, alpha-beta T cell	6.08e-11	11
myeloid cell	6.00e-09	112
common myeloid progenitor	6.00e-09	112
CD4-positive, alpha-beta T cell	5.81e-07	6

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.47e-10	112
blood	3.65e-10	15
haemolymphatic fluid	3.65e-10	15
organism substance	3.65e-10	15
hematopoietic system	1.20e-09	102
blood island	1.20e-09	102

Disease

Ontology term	p-value	n
hematologic cancer	9.58e-14	51
immune system cancer	9.58e-14	51
leukemia	5.12e-10	39
lymphoma	2.89e-08	10

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
CHD2#1106	4	4.13760913364674	0.0113650969219832	0.0416623151082836
CTCFL#140690	4	7.89858974358974	0.00107835657510799	0.00761322803675411
ETS1#2113	4	3.89150436888093	0.0140779870843833	0.0494016159231874
HDAC2#3066	4	5.3662480946505	0.00449304567601398	0.0212560788801062
MEF2A#4205	5	9.37161545482203	8.6760671028562e-05	0.00129946905514872
NFKB1#4790	6	3.2928380545163	0.0039127525205927	0.0190678904623294
PAX5#5079	5	3.33478276558891	0.00985362449367583	0.0370274057674598
RAD21#5885	4	4.14201355818253	0.0113227647567404	0.0415304568528908
SMC3#9126	4	6.01797313797314	0.00295796391668531	0.0157696168195353
THAP1#55145	4	12.5476578411405	0.000185650056088679	0.00224697024079795
TRIM28#10155	4	7.43621001810501	0.00135140622114295	0.00889964779178694
USF1#7391	5	3.18074963860398	0.0120650064178445	0.0437884766914535
ZEB1#6935	4	6.75537280701754	0.00193155612719453	0.0113516285165759
ZNF143#7702	4	5.40035062089116	0.00439099655010477	0.0208100598401049
ZNF263#10127	5	4.11092081850534	0.00394439922578783	0.0189602389074449

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.