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Coexpression cluster:C496: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0852944574994353,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.338508012354035,0.143954471904592,0.260645135633498,0.368750126335451,0.36242386112225,0.527273946548287,0.469566853250347,0.347430530801241,0.39322930351941,0.367207409328123,0.371810022664044,0.27798473109364,0.309731231421723,0.448523437344291,0.50661327355052,0.43756325503545,0.420145969880685,0.496974821301028,0.310768747319633,0.25362035008045,0.403614953289289,0.532167126540495,0.355087084824636,0.356840429473398,0.362136806900612,0.462533370184438,0.279541636226675,0.357909343173742,0.352048786074314,0.339230015971761,0.53950064512279,0.256820409353761,0.102927476286267,0.236567998427762,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.158803529189909,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.297794159634267,0.155717062297439,0.215297814247436,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.150306889650249,0.155769630002388,0.120634028603673,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.178242227335072,0.246655432029025,0.195802046114694,0.169222730114762,0.260721042151348,0,0.187529586342753,0.253610608288505,0,0,0,0,0,0.0298469850284923,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.191050583413854,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0368115019473605,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.174979787616842,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390109377342095,0.0767764493450943,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.092743246865863,0.876418764653734,0.897093146490667,0,0,0,0,0,0.12605352776203,0.0300822291072195,0,0,0,0,0,0,0,0,0,0.343928797661606,0|full_id=C496_thymus_CD4_CD8_hairy_vein_chronic_Peripheral|gostat_on_coexpression_clusters=GO:0032236!positive regulation of calcium ion transport via store-operated calcium channel!0.00473317045069122!6786$GO:0032237!activation of store-operated calcium channel activity!0.00473317045069122!6786$GO:0043270!positive regulation of ion transport!0.00473317045069122!6786$GO:0032234!regulation of calcium ion transport via store-operated calcium channel!0.00473317045069122!6786$GO:0051928!positive regulation of calcium ion transport!0.00473317045069122!6786$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.011831532856717!399$GO:0005513!detection of calcium ion!0.0135209557288322!6786$GO:0005095!GTPase inhibitor activity!0.0147876746201048!399$GO:0051924!regulation of calcium ion transport!0.015772590875712!6786$GO:0043269!regulation of ion transport!0.0193538515139206!6786$GO:0009593!detection of chemical stimulus!0.0193538515139206!6786$GO:0017048!Rho GTPase binding!0.0315266113806201!399$GO:0051050!positive regulation of transport!0.0330931953761501!6786$GO:0030217!T cell differentiation!0.0330931953761501!399$GO:0019210!kinase inhibitor activity!0.0330931953761501!399$GO:0030176!integral to endoplasmic reticulum membrane!0.038264986352189!6786$GO:0002376!immune system process!0.038264986352189!399;51561$GO:0031227!intrinsic to endoplasmic reticulum membrane!0.0397855755213595!6786$GO:0030098!lymphocyte differentiation!0.0397855755213595!399$GO:0017016!Ras GTPase binding!0.043249602836329!399$GO:0051606!detection of stimulus!0.043249602836329!6786$GO:0031267!small GTPase binding!0.043249602836329!399$GO:0002521!leukocyte differentiation!0.043249602836329!399$GO:0051020!GTPase binding!0.043249602836329!399$GO:0009615!response to virus!0.043249602836329!51561$GO:0042110!T cell activation!0.043249602836329!399$GO:0009968!negative regulation of signal transduction!0.043249602836329!399$GO:0048771!tissue remodeling!0.043249602836329!51561$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.043249602836329!399$GO:0051049!regulation of transport!0.043249602836329!6786$GO:0045087!innate immune response!0.0433713217382676!51561$GO:0019207!kinase regulator activity!0.0449538569971292!399$GO:0031301!integral to organelle membrane!0.048180952305821!6786$GO:0007249!I-kappaB kinase/NF-kappaB 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|full_id=C496_thymus_CD4_CD8_hairy_vein_chronic_Peripheral
|gostat_on_coexpression_clusters=GO:0032236!positive regulation of calcium ion transport via store-operated calcium channel!0.00473317045069122!6786$GO:0032237!activation of store-operated calcium channel activity!0.00473317045069122!6786$GO:0043270!positive regulation of ion transport!0.00473317045069122!6786$GO:0032234!regulation of calcium ion transport via store-operated calcium channel!0.00473317045069122!6786$GO:0051928!positive regulation of calcium ion transport!0.00473317045069122!6786$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.011831532856717!399$GO:0005513!detection of calcium ion!0.0135209557288322!6786$GO:0005095!GTPase inhibitor activity!0.0147876746201048!399$GO:0051924!regulation of calcium ion transport!0.015772590875712!6786$GO:0043269!regulation of ion transport!0.0193538515139206!6786$GO:0009593!detection of chemical stimulus!0.0193538515139206!6786$GO:0017048!Rho GTPase binding!0.0315266113806201!399$GO:0051050!positive regulation of transport!0.0330931953761501!6786$GO:0030217!T cell differentiation!0.0330931953761501!399$GO:0019210!kinase inhibitor activity!0.0330931953761501!399$GO:0030176!integral to endoplasmic reticulum membrane!0.038264986352189!6786$GO:0002376!immune system process!0.038264986352189!399;51561$GO:0031227!intrinsic to endoplasmic reticulum membrane!0.0397855755213595!6786$GO:0030098!lymphocyte differentiation!0.0397855755213595!399$GO:0017016!Ras GTPase binding!0.043249602836329!399$GO:0051606!detection of stimulus!0.043249602836329!6786$GO:0031267!small GTPase binding!0.043249602836329!399$GO:0002521!leukocyte differentiation!0.043249602836329!399$GO:0051020!GTPase binding!0.043249602836329!399$GO:0009615!response to virus!0.043249602836329!51561$GO:0042110!T cell activation!0.043249602836329!399$GO:0009968!negative regulation of signal transduction!0.043249602836329!399$GO:0048771!tissue remodeling!0.043249602836329!51561$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.043249602836329!399$GO:0051049!regulation of transport!0.043249602836329!6786$GO:0045087!innate immune response!0.0433713217382676!51561$GO:0019207!kinase regulator activity!0.0449538569971292!399$GO:0031301!integral to organelle membrane!0.048180952305821!6786$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.048180952305821!399
|id=C496
|ontology_enrichment_celltype=CL:0000738!3.61e-25!140;CL:0000542!3.59e-23!53;CL:0000051!3.59e-23!53;CL:0000838!8.92e-23!52;CL:0002087!1.27e-21!119;CL:0000037!1.81e-18!172;CL:0000566!1.81e-18!172;CL:0002031!2.81e-18!124;CL:0000084!6.05e-18!25;CL:0000827!6.05e-18!25;CL:0000988!1.02e-16!182;CL:0002032!1.34e-15!165;CL:0000837!1.34e-15!165;CL:0000791!1.17e-14!18;CL:0000789!1.17e-14!18;CL:0002420!1.17e-14!18;CL:0002419!1.17e-14!18;CL:0000790!1.17e-14!18;CL:0000625!1.13e-09!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.93e-20!115;UBERON:0002390!6.72e-09!102;UBERON:0003061!6.72e-09!102;UBERON:0000178!1.54e-08!15;UBERON:0000179!1.54e-08!15;UBERON:0000463!1.54e-08!15;UBERON:0002193!1.61e-07!112
}}

Latest revision as of 11:24, 17 September 2013


Full id: C496_thymus_CD4_CD8_hairy_vein_chronic_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:3968515..3968532,+p3@STIM1
Hg19::chr14:22265490..22265505,+p4@TRAV8-1
Hg19::chr14:22320634..22320645,+p1@TRAV8-3
Hg19::chr15:22466523..22466550,-p1@uc001yui.1
Hg19::chr16:56742627..56742637,+p@chr16:56742627..56742637
+
Hg19::chr17:78717112..78717159,+p2@RPTOR
Hg19::chr2:95740646..95740655,+p@chr2:95740646..95740655
+
Hg19::chr4:40192677..40192712,+p4@RHOH
Hg19::chr6:128222238..128222249,-p5@THEMIS
Hg19::chr7:142028105..142028159,+p1@TRBV6-1
Hg19::chr7:142162390..142162425,-p1@TRBV6-6
Hg19::chr7:142180964..142180969,-p4@TRBV6-5
Hg19::chr7:142180978..142181006,-p1@TRBV6-5
Hg19::chr7:142198109..142198132,-p2@TRBV11-2
Hg19::chr7:142334728..142334737,+p1@AB306258
Hg19::chr7:142344506..142344509,+p1@AJ296363
p1@AJ296373
p1@HM236738
Hg19::chr7:142498815..142498839,+p1@AJ568018
Hg19::chr7:142507125..142507136,+p@chr7:142507125..142507136
+
Hg19::chr9:33446618..33446630,+p@chr9:33446618..33446630
+


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

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

GO IDGO nameFDR corrected p-value
GO:0032236positive regulation of calcium ion transport via store-operated calcium channel0.00473317045069122
GO:0032237activation of store-operated calcium channel activity0.00473317045069122
GO:0043270positive regulation of ion transport0.00473317045069122
GO:0032234regulation of calcium ion transport via store-operated calcium channel0.00473317045069122
GO:0051928positive regulation of calcium ion transport0.00473317045069122
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.011831532856717
GO:0005513detection of calcium ion0.0135209557288322
GO:0005095GTPase inhibitor activity0.0147876746201048
GO:0051924regulation of calcium ion transport0.015772590875712
GO:0043269regulation of ion transport0.0193538515139206
GO:0009593detection of chemical stimulus0.0193538515139206
GO:0017048Rho GTPase binding0.0315266113806201
GO:0051050positive regulation of transport0.0330931953761501
GO:0030217T cell differentiation0.0330931953761501
GO:0019210kinase inhibitor activity0.0330931953761501
GO:0030176integral to endoplasmic reticulum membrane0.038264986352189
GO:0002376immune system process0.038264986352189
GO:0031227intrinsic to endoplasmic reticulum membrane0.0397855755213595
GO:0030098lymphocyte differentiation0.0397855755213595
GO:0017016Ras GTPase binding0.043249602836329
GO:0051606detection of stimulus0.043249602836329
GO:0031267small GTPase binding0.043249602836329
GO:0002521leukocyte differentiation0.043249602836329
GO:0051020GTPase binding0.043249602836329
GO:0009615response to virus0.043249602836329
GO:0042110T cell activation0.043249602836329
GO:0009968negative regulation of signal transduction0.043249602836329
GO:0048771tissue remodeling0.043249602836329
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.043249602836329
GO:0051049regulation of transport0.043249602836329
GO:0045087innate immune response0.0433713217382676
GO:0019207kinase regulator activity0.0449538569971292
GO:0031301integral to organelle membrane0.048180952305821
GO:0007249I-kappaB kinase/NF-kappaB cascade0.048180952305821



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>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell2.79e-5118
alpha-beta T cell2.79e-5118
immature T cell2.79e-5118
mature T cell2.79e-5118
immature alpha-beta T cell2.79e-5118
T cell7.72e-4025
pro-T cell7.72e-4025
CD8-positive, alpha-beta T cell7.78e-3611
lymphoid lineage restricted progenitor cell2.45e-2352
lymphocyte8.57e-2353
common lymphoid progenitor8.57e-2353
nucleate cell9.14e-2255
CD4-positive, alpha-beta T cell2.95e-206
nongranular leukocyte1.38e-11115
naive T cell1.71e-113
natural killer cell2.09e-103
pro-NK cell2.09e-103
single nucleate cell5.92e-103
mononuclear cell5.92e-103
leukocyte7.85e-10136
regulatory T cell3.44e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell3.44e-082
naive regulatory T cell3.44e-082
hematopoietic lineage restricted progenitor cell5.81e-08120
hematopoietic stem cell7.41e-07168
angioblastic mesenchymal cell7.41e-07168
Uber Anatomy
Ontology termp-valuen
blood1.91e-1915
haemolymphatic fluid1.91e-1915
organism substance1.91e-1915
hemopoietic organ3.59e-127
immune organ3.59e-127
thymus4.85e-094
hemolymphoid system gland4.85e-094
thymic region4.85e-094
pharyngeal gland4.85e-094
thymus primordium4.85e-094


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

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.000148818
MA0004.10.563888
MA0006.10.0925234
MA0007.10.180248
MA0009.10.580032
MA0014.14.97928e-05
MA0017.10.114723
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.269828
MA0040.10.507819
MA0041.10.595574
MA0042.11.03458
MA0043.10.580321
MA0046.10.570066
MA0048.10.131175
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.194883
MA0056.10
MA0057.10.0434899
MA0058.10.407083
MA0059.10.805771
MA0060.10.0387582
MA0061.10.121714
MA0063.10
MA0066.11.36491
MA0067.10.879057
MA0068.10.0841176
MA0069.10.566544
MA0070.10.556335
MA0071.11.25272
MA0072.10.552241
MA0073.11.28654e-06
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.915792
MA0081.10.129245
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.0166254
MA0089.10
MA0090.10.455738
MA0091.13.1902
MA0092.10.504823
MA0093.10.313082
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.11.03031
MA0105.10.00666152
MA0106.10.302526
MA0107.10.0591705
MA0108.20.432749
MA0109.10
MA0111.11.48573
MA0113.10.315797
MA0114.10.456488
MA0115.10.805883
MA0116.10.219141
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.10.766407
MA0125.11.64333
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.755761
MA0139.10.792683
MA0140.10.238066
MA0141.10.128074
MA0142.11.05085
MA0143.10.315941
MA0144.10.189563
MA0145.10.0661076
MA0146.10.00163852
MA0147.10.223797
MA0148.10.606512
MA0149.10.230803
MA0062.20.027823
MA0035.20.668495
MA0039.20.00730638
MA0138.20.347473
MA0002.21.32966
MA0137.20.105044
MA0104.20.0384802
MA0047.20.292798
MA0112.20.256517
MA0065.20.468021
MA0150.10.145358
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.214105
MA0155.10.0530942
MA0156.11.16068
MA0157.10.99963
MA0158.10
MA0159.10.224647
MA0160.11.18515
MA0161.10
MA0162.10.00017322
MA0163.10.178355
MA0164.10.32594
MA0080.21.07751
MA0018.20.30364
MA0099.20.243305
MA0079.22.0946e-06
MA0102.21.09681
MA0258.10.177641
MA0259.10.235101
MA0442.10



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

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

This analysis result is provided for C0 - C305 clusters.

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