Coexpression cluster:C911

Full id: C911_cord_CD8_Natural_mycosis_Basophils_Peripheral_CD4

Phase1 CAGE Peaks

Hg19::chr16:27413488..27413517,+	p1@IL21R
Hg19::chr16:27413524..27413547,+	p2@IL21R
Hg19::chr16:27413589..27413601,+	p5@IL21R
Hg19::chr16:27413815..27413889,+	p4@IL21R
Hg19::chr17:45810594..45810608,+	p1@TBX21
Hg19::chr17:45810816..45810838,+	p2@TBX21
Hg19::chr3:193311668..193311697,-	p@chr3:193311668..193311697 -
Hg19::chr6:106968697..106968723,-	p@chr6:106968697..106968723 -
Hg19::chr6:90790583..90790604,-	p@chr6:90790583..90790604 -

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:0046649	lymphocyte activation	0.00107147062286589
GO:0045321	leukocyte activation	0.00107147062286589
GO:0001775	cell activation	0.00107147062286589
GO:0019977	interleukin-21 binding	0.00107147062286589
GO:0001532	interleukin-21 receptor activity	0.00107147062286589
GO:0048304	positive regulation of isotype switching to IgG isotypes	0.00267855827937379
GO:0048302	regulation of isotype switching to IgG isotypes	0.00267855827937379
GO:0048291	isotype switching to IgG isotypes	0.00267855827937379
GO:0045830	positive regulation of isotype switching	0.00357130590335091
GO:0045191	regulation of isotype switching	0.00420872932521112
GO:0002208	somatic diversification of immunoglobulins during immune response	0.00420872932521112
GO:0002381	immunoglobulin production during immune response	0.00420872932521112
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.00420872932521112
GO:0045190	isotype switching	0.00420872932521112
GO:0016447	somatic recombination of immunoglobulin gene segments	0.00438219215402637
GO:0016445	somatic diversification of immunoglobulins	0.00438219215402637
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.00438219215402637
GO:0016444	somatic cell DNA recombination	0.00438219215402637
GO:0002200	somatic diversification of immune receptors	0.00438219215402637
GO:0030101	natural killer cell activation	0.00438219215402637
GO:0050871	positive regulation of B cell activation	0.00438219215402637
GO:0002377	immunoglobulin production	0.00438219215402637
GO:0050864	regulation of B cell activation	0.00582115290182016
GO:0002440	production of molecular mediator of immune response	0.00602471583669748
GO:0002376	immune system process	0.00605459280668687
GO:0004907	interleukin receptor activity	0.00700236669613786
GO:0019965	interleukin binding	0.00793226354335589
GO:0051251	positive regulation of lymphocyte activation	0.00927910822702546
GO:0016064	immunoglobulin mediated immune response	0.00927910822702546
GO:0019724	B cell mediated immunity	0.00927910822702546
GO:0042113	B cell activation	0.0105325787794911
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0112655238259798
GO:0002449	lymphocyte mediated immunity	0.0112655238259798
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0112655238259798
GO:0002250	adaptive immune response	0.0112655238259798
GO:0051249	regulation of lymphocyte activation	0.0112655238259798
GO:0002443	leukocyte mediated immunity	0.0112655238259798
GO:0050865	regulation of cell activation	0.0112655238259798
GO:0050776	regulation of immune response	0.0130476750734828
GO:0019955	cytokine binding	0.0130476750734828
GO:0002682	regulation of immune system process	0.0130476750734828
GO:0002252	immune effector process	0.0140086525896998
GO:0002520	immune system development	0.022614900670125
GO:0006310	DNA recombination	0.0239171348972863
GO:0051239	regulation of multicellular organismal process	0.0328435206715787

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
leukocyte	5.87e-75	136
nongranular leukocyte	2.39e-64	115
hematopoietic stem cell	1.07e-59	168
angioblastic mesenchymal cell	1.07e-59	168
hematopoietic cell	2.32e-59	177
hematopoietic lineage restricted progenitor cell	5.67e-59	120
hematopoietic oligopotent progenitor cell	4.97e-54	161
hematopoietic multipotent progenitor cell	4.97e-54	161
lymphocyte	1.33e-40	53
common lymphoid progenitor	1.33e-40	53
lymphoid lineage restricted progenitor cell	5.86e-40	52
nucleate cell	2.27e-38	55
myeloid leukocyte	6.87e-25	72
macrophage dendritic cell progenitor	3.16e-22	61
T cell	3.54e-22	25
pro-T cell	3.54e-22	25
classical monocyte	2.81e-21	42
CD14-positive, CD16-negative classical monocyte	2.81e-21	42
monopoietic cell	7.72e-21	59
monocyte	7.72e-21	59
monoblast	7.72e-21	59
promonocyte	7.72e-21	59
granulocyte monocyte progenitor cell	8.99e-21	67
defensive cell	1.24e-20	48
phagocyte	1.24e-20	48
mature alpha-beta T cell	2.15e-19	18
alpha-beta T cell	2.15e-19	18
immature T cell	2.15e-19	18
mature T cell	2.15e-19	18
immature alpha-beta T cell	2.15e-19	18
myeloid lineage restricted progenitor cell	6.51e-19	66
myeloid cell	5.22e-18	108
common myeloid progenitor	5.22e-18	108
lymphocyte of B lineage	1.38e-15	24
pro-B cell	1.38e-15	24
CD8-positive, alpha-beta T cell	2.61e-12	11
mesenchymal cell	3.22e-11	354
connective tissue cell	2.27e-10	361
B cell	1.25e-08	14
CD4-positive, alpha-beta T cell	4.26e-08	6
circulating cell	4.26e-08	6
motile cell	4.33e-08	386
dendritic cell	1.68e-07	10

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.73e-35	98
blood island	6.73e-35	98
hemolymphoid system	1.03e-31	108
immune system	2.60e-20	93
bone marrow	3.83e-18	76
bone element	3.54e-17	82
blood	2.61e-15	15
haemolymphatic fluid	2.61e-15	15
organism substance	2.61e-15	15
skeletal element	3.30e-14	90
skeletal system	7.38e-12	100
connective tissue	3.06e-09	371
lateral plate mesoderm	2.20e-08	203
adult organism	5.02e-07	114
hemopoietic organ	5.24e-07	7
immune organ	5.24e-07	7

Disease

Ontology term	p-value	n
lymphoma	6.03e-07	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
EBF1#1879	4	3.95842970958622	0.01255739025408	0.0454176922269658
MEF2A#4205	4	8.33032484873069	0.000821150143030061	0.00625483916475214
NFKB1#4790	6	3.65870894946256	0.00185064964860272	0.010935219159854
PAX5#5079	6	4.44637702078522	0.000632270008817587	0.00519132448513364
POU2F2#5452	7	7.08254093379974	5.66141070992737e-06	0.000170542853514308
TCF12#6938	5	5.90803605677023	0.000668943553105202	0.00546494021767477

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.