Coexpression cluster:C1218

Full id: C1218_hairy_plasma_lymphoma_xeroderma_hereditary_mycosis_splenic

Phase1 CAGE Peaks

Hg19::chr16:29656517..29656522,-	p@chr16:29656517..29656522 -
Hg19::chr1:32716592..32716596,+	p5@LCK
Hg19::chr20:52675557..52675561,-	p4@BCAS1
Hg19::chr4:36334205..36334210,-	p@chr4:36334205..36334210 -
Hg19::chr6:109196481..109196488,+	p@chr6:109196481..109196488 +
Hg19::chr6:160351875..160351879,-	p@chr6:160351875..160351879 -
Hg19::chr8:101512336..101512341,-	p@chr8:101512336..101512341 -

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:0042610	CD8 receptor binding	0.00549074903622083
GO:0050862	positive regulation of T cell receptor signaling pathway	0.00549074903622083
GO:0042609	CD4 receptor binding	0.00549074903622083
GO:0051117	ATPase binding	0.00549074903622083
GO:0006882	cellular zinc ion homeostasis	0.00549074903622083
GO:0055069	zinc ion homeostasis	0.00549074903622083
GO:0043548	phosphoinositide 3-kinase binding	0.00549074903622083
GO:0001948	glycoprotein binding	0.00549074903622083
GO:0050857	positive regulation of antigen receptor-mediated signaling pathway	0.00549074903622083
GO:0000242	pericentriolar material	0.00549074903622083
GO:0050856	regulation of T cell receptor signaling pathway	0.00549074903622083
GO:0051283	negative regulation of sequestering of calcium ion	0.00575204393640925
GO:0051282	regulation of sequestering of calcium ion	0.00575204393640925
GO:0051209	release of sequestered calcium ion into cytosol	0.00575204393640925
GO:0051208	sequestering of calcium ion	0.00629111284022556
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.00629111284022556
GO:0051238	sequestering of metal ion	0.00769702166833902
GO:0050852	T cell receptor signaling pathway	0.0095055909313886
GO:0042169	SH2 domain binding	0.00953487963183759
GO:0044450	microtubule organizing center part	0.0115734324519592
GO:0050851	antigen receptor-mediated signaling pathway	0.0129384792222954
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0132823318112429
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0132823318112429
GO:0002757	immune response-activating signal transduction	0.0132823318112429
GO:0002764	immune response-regulating signal transduction	0.0132823318112429
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0142244370855518
GO:0050870	positive regulation of T cell activation	0.0142244370855518
GO:0030217	T cell differentiation	0.0142244370855518
GO:0051235	maintenance of localization	0.0142244370855518
GO:0006919	caspase activation	0.0149284042553036
GO:0045121	lipid raft	0.0149284042553036
GO:0043280	positive regulation of caspase activity	0.0155468175678466
GO:0051251	positive regulation of lymphocyte activation	0.0155468175678466
GO:0050863	regulation of T cell activation	0.0172038426275883
GO:0043281	regulation of caspase activity	0.0172038426275883
GO:0042493	response to drug	0.0172038426275883
GO:0030098	lymphocyte differentiation	0.0172038426275883
GO:0004722	protein serine/threonine phosphatase activity	0.0172038426275883
GO:0051480	cytosolic calcium ion homeostasis	0.0173694565847348
GO:0007204	elevation of cytosolic calcium ion concentration	0.0173694565847348
GO:0002253	activation of immune response	0.0173694565847348
GO:0008022	protein C-terminus binding	0.0173694565847348
GO:0051345	positive regulation of hydrolase activity	0.0173694565847348
GO:0051249	regulation of lymphocyte activation	0.0173694565847348
GO:0050865	regulation of cell activation	0.0178762817634228
GO:0019901	protein kinase binding	0.0180143473637898
GO:0050778	positive regulation of immune response	0.0180143473637898
GO:0002684	positive regulation of immune system process	0.0180143473637898
GO:0008632	apoptotic program	0.0180970681862679
GO:0002521	leukocyte differentiation	0.0180970681862679
GO:0050776	regulation of immune response	0.0186156389784673
GO:0042110	T cell activation	0.0186156389784673
GO:0019900	kinase binding	0.0186156389784673
GO:0002682	regulation of immune system process	0.0186156389784673
GO:0051240	positive regulation of multicellular organismal process	0.0191896170851969
GO:0006874	cellular calcium ion homeostasis	0.0204527827727977
GO:0055074	calcium ion homeostasis	0.0204527827727977
GO:0006875	cellular metal ion homeostasis	0.0209496874891393
GO:0055065	metal ion homeostasis	0.0209496874891393
GO:0019904	protein domain specific binding	0.0212493622807121
GO:0005813	centrosome	0.0212493622807121
GO:0005815	microtubule organizing center	0.0238175112989571
GO:0046649	lymphocyte activation	0.0247121557886227
GO:0030097	hemopoiesis	0.025265444591113
GO:0048534	hemopoietic or lymphoid organ development	0.0266282153137071
GO:0045321	leukocyte activation	0.0266282153137071
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0266282153137071
GO:0002520	immune system development	0.0266282153137071
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0266282153137071
GO:0030003	cellular cation homeostasis	0.0286789366588777
GO:0055080	cation homeostasis	0.0286978621515081
GO:0001775	cell activation	0.0288865464751273
GO:0006917	induction of apoptosis	0.0288865464751273
GO:0012502	induction of programmed cell death	0.0288865464751273
GO:0055082	cellular chemical homeostasis	0.0312844536056327
GO:0006873	cellular ion homeostasis	0.0312844536056327
GO:0043085	positive regulation of catalytic activity	0.0327530472383582
GO:0043065	positive regulation of apoptosis	0.0327530472383582
GO:0043068	positive regulation of programmed cell death	0.0327530472383582
GO:0050801	ion homeostasis	0.0334674497335767
GO:0051239	regulation of multicellular organismal process	0.0342871919098899
GO:0048878	chemical homeostasis	0.0361962874839148
GO:0019899	enzyme binding	0.0361962874839148
GO:0004713	protein-tyrosine kinase activity	0.0361962874839148
GO:0051336	regulation of hydrolase activity	0.0361962874839148
GO:0004721	phosphoprotein phosphatase activity	0.0364713582468456
GO:0019725	cellular homeostasis	0.0431538693944755
GO:0007265	Ras protein signal transduction	0.0491068728919253
GO:0016791	phosphoric monoester hydrolase activity	0.0492251115653811

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
lymphocyte of B lineage	4.79e-33	24
pro-B cell	4.79e-33	24
lymphocyte	5.12e-25	53
common lymphoid progenitor	5.12e-25	53
nucleate cell	5.55e-24	55
lymphoid lineage restricted progenitor cell	2.37e-22	52
precursor B cell	1.87e-18	3
mature B cell	3.28e-13	2
pre-B-II cell	3.28e-13	2
transitional stage B cell	3.28e-13	2
small pre-B-II cell	3.28e-13	2
immature B cell	3.28e-13	2
hematopoietic cell	3.27e-11	177
nongranular leukocyte	1.37e-09	115
circulating cell	4.27e-09	6
leukocyte	9.47e-09	136
hematopoietic stem cell	1.79e-08	168
angioblastic mesenchymal cell	1.79e-08	168
hematopoietic oligopotent progenitor cell	6.61e-08	161
hematopoietic multipotent progenitor cell	6.61e-08	161
hematopoietic lineage restricted progenitor cell	7.95e-08	120
antibody secreting cell	1.55e-07	1
plasma cell	1.55e-07	1
plasmablast	1.55e-07	1
B-1 B cell	2.37e-07	1
CD34-positive, CD38-negative hematopoietic stem cell	3.60e-07	1

Uber Anatomy

Ontology term	p-value	n
lymph node	2.52e-07	1

Disease

Ontology term	p-value	n
lymphoma	1.41e-36	10
hematologic cancer	3.07e-14	51
immune system cancer	3.07e-14	51
anemia	1.65e-07	1
non-Hodgkin lymphoma	1.75e-07	1
cutaneous T cell lymphoma	1.75e-07	1
mycosis fungoides	1.75e-07	1
lymphatic system cancer	2.37e-07	1
lymphosarcoma	2.37e-07	1
genetic disease	3.01e-07	1
monogenic disease	3.01e-07	1
xeroderma pigmentosum	3.01e-07	1
acute leukemia	4.57e-07	1
papillary adenocarcinoma	4.85e-07	1

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
BATF#10538	3	10.4390579109873	0.0021372507929898	0.0123499134430155
IRF4#3662	3	9.39193400860463	0.00289381368834148	0.0156456493139046
MEF2A#4205	3	8.03281324699031	0.00451639783467502	0.0213549471865096

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.