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Coexpression cluster:C580

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Full id: C580_chronic_thymus_Hodgkin_acute_iPS_vein_Burkitt



Phase1 CAGE Peaks

Hg19::chr10:15183694..15183716,-p4@NMT2
Hg19::chr16:89165074..89165092,+p5@ACSF3
Hg19::chr1:198488823..198488834,-p@chr1:198488823..198488834
-
Hg19::chr1:198488915..198488926,-p@chr1:198488915..198488926
-
Hg19::chr1:32398355..32398370,-p@chr1:32398355..32398370
-
Hg19::chr1:32403130..32403147,-p@chr1:32403130..32403147
-
Hg19::chr1:32739715..32739730,+p3@LCK
Hg19::chr1:32739735..32739746,+p4@LCK
Hg19::chr2:136578012..136578026,+p3@LOC100507600
Hg19::chr4:109084747..109084756,-p@chr4:109084747..109084756
-
Hg19::chr4:109084760..109084771,-p@chr4:109084760..109084771
-
Hg19::chr4:145580820..145580831,+p@chr4:145580820..145580831
+
Hg19::chr4:40192723..40192736,+p10@RHOH
Hg19::chr7:2106220..2106240,-p@chr7:2106220..2106240
-
Hg19::chrX:123538949..123538959,-p@chrX:123538949..123538959
-


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:0030217T cell differentiation0.00187293756729479
GO:0030098lymphocyte differentiation0.00230026342169233
GO:0002521leukocyte differentiation0.0027079740611187
GO:0042110T cell activation0.0027079740611187
GO:0042610CD8 receptor binding0.00374128978289831
GO:0046649lymphocyte activation0.00374128978289831
GO:0030097hemopoiesis0.00374128978289831
GO:0048534hemopoietic or lymphoid organ development0.00374128978289831
GO:0045321leukocyte activation0.00374128978289831
GO:0002520immune system development0.00374128978289831
GO:0001775cell activation0.00398500640042086
GO:0050862positive regulation of T cell receptor signaling pathway0.00398500640042086
GO:0042609CD4 receptor binding0.00398500640042086
GO:0051117ATPase binding0.00517959338214823
GO:0006882cellular zinc ion homeostasis0.00517959338214823
GO:0009249protein lipoylation0.00517959338214823
GO:0055069zinc ion homeostasis0.00517959338214823
GO:0019899enzyme binding0.00517959338214823
GO:0043548phosphoinositide 3-kinase binding0.00517959338214823
GO:0018065protein-cofactor linkage0.00517959338214823
GO:0006499N-terminal protein myristoylation0.00517959338214823
GO:0004379glycylpeptide N-tetradecanoyltransferase activity0.00517959338214823
GO:0018319protein amino acid myristoylation0.00517959338214823
GO:0018377protein myristoylation0.00517959338214823
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.00517959338214823
GO:0001948glycoprotein binding0.00517959338214823
GO:0050857positive regulation of antigen receptor-mediated signaling pathway0.00517959338214823
GO:0000242pericentriolar material0.00517959338214823
GO:0019107myristoyltransferase activity0.00517959338214823
GO:0050856regulation of T cell receptor signaling pathway0.00517959338214823
GO:0006498N-terminal protein lipidation0.00584766978870286
GO:0051283negative regulation of sequestering of calcium ion0.00609310113743239
GO:0051282regulation of sequestering of calcium ion0.00609310113743239
GO:0051209release of sequestered calcium ion into cytosol0.00609310113743239
GO:0005095GTPase inhibitor activity0.00699821430729356
GO:0051208sequestering of calcium ion0.00699821430729356
GO:0050854regulation of antigen receptor-mediated signaling pathway0.00699821430729356
GO:0051238sequestering of metal ion0.00885709258062343
GO:0018409peptide or protein amino-terminal blocking0.0092934224497359
GO:0050852T cell receptor signaling pathway0.0110012908396699
GO:0042169SH2 domain binding0.0110932487759747
GO:0031365N-terminal protein amino acid modification0.0110932487759747
GO:0044450microtubule organizing center part0.0138420057461097
GO:0050851antigen receptor-mediated signaling pathway0.0158772036844918
GO:0002429immune response-activating cell surface receptor signaling pathway0.0167375395149149
GO:0043543protein amino acid acylation0.0167375395149149
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0167375395149149
GO:0002757immune response-activating signal transduction0.0167375395149149
GO:0017048Rho GTPase binding0.0167375395149149
GO:0007264small GTPase mediated signal transduction0.0167375395149149
GO:0002764immune response-regulating signal transduction0.0167375395149149
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0196329023784135
GO:0050870positive regulation of T cell activation0.0196329023784135
GO:0051235maintenance of localization0.0196329023784135
GO:0019210kinase inhibitor activity0.0197452133423667
GO:0006919caspase activation0.0208632269515984
GO:0045121lipid raft0.0208632269515984
GO:0043280positive regulation of caspase activity0.0222824936971152
GO:0051251positive regulation of lymphocyte activation0.0223419340034754
GO:0006497protein amino acid lipidation0.0228291034560098
GO:0042158lipoprotein biosynthetic process0.0229369435690701
GO:0048513organ development0.0229369435690701
GO:0050863regulation of T cell activation0.0241969489110459
GO:0043281regulation of caspase activity0.024221511413098
GO:0042493response to drug0.0250379984664169
GO:0004722protein serine/threonine phosphatase activity0.0254392012708153
GO:0051480cytosolic calcium ion homeostasis0.0265722426642582
GO:0007204elevation of cytosolic calcium ion concentration0.0265722426642582
GO:0002253activation of immune response0.0265722426642582
GO:0008022protein C-terminus binding0.0272315094563042
GO:0051345positive regulation of hydrolase activity0.0272315094563042
GO:0051249regulation of lymphocyte activation0.0272315094563042
GO:0017016Ras GTPase binding0.0272315094563042
GO:0050865regulation of cell activation0.0277089471060443
GO:0002376immune system process0.0277089471060443
GO:0019901protein kinase binding0.0277421206030372
GO:0042157lipoprotein metabolic process0.0277421206030372
GO:0031267small GTPase binding0.0277421206030372
GO:0050778positive regulation of immune response0.0277421206030372
GO:0002684positive regulation of immune system process0.0277421206030372
GO:0008632apoptotic program0.0280059165722411
GO:0016410N-acyltransferase activity0.0280059165722411
GO:0051020GTPase binding0.0299891491571014
GO:0050776regulation of immune response0.0299891491571014
GO:0019900kinase binding0.0299891491571014
GO:0002682regulation of immune system process0.0299891491571014
GO:0009968negative regulation of signal transduction0.0307661597671867
GO:0051240positive regulation of multicellular organismal process0.0307661597671867
GO:0048731system development0.0309378657180192
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0309378657180192
GO:0006874cellular calcium ion homeostasis0.0324956904139546
GO:0055074calcium ion homeostasis0.0324956904139546
GO:0018193peptidyl-amino acid modification0.0330107331571969
GO:0019207kinase regulator activity0.0330107331571969
GO:0006875cellular metal ion homeostasis0.0330107331571969
GO:0055065metal ion homeostasis0.0330107331571969
GO:0019904protein domain specific binding0.0337269077482176
GO:0005813centrosome0.0339054720560488
GO:0048869cellular developmental process0.034846178409539
GO:0030154cell differentiation0.034846178409539
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0354329812943836
GO:0005815microtubule organizing center0.0370918001383408
GO:0007242intracellular signaling cascade0.0396255033883722
GO:0048856anatomical structure development0.0407925640331565
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0440565636089676
GO:0055066di-, tri-valent inorganic cation homeostasis0.044362402403937
GO:0030003cellular cation homeostasis0.047914710907547
GO:0055080cation homeostasis0.047914710907547
GO:0043687post-translational protein modification0.047914710907547
GO:0006917induction of apoptosis0.0492119839151446
GO:0012502induction of programmed cell death0.0492119839151446
GO:0007275multicellular organismal development0.0492119839151446



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>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ5.55e-157
immune organ5.55e-157
thymus2.08e-124
hemolymphoid system gland2.08e-124
thymic region2.08e-124
pharyngeal gland2.08e-124
thymus primordium2.08e-124
tonsil4.31e-121
mucosa-associated lymphoid tissue4.31e-121
lymphoid tissue4.31e-121
tonsillar ring4.31e-121
neck8.93e-1110
chordate pharynx1.13e-1010
pharyngeal region of foregut1.13e-1010
pharynx9.40e-1011
pharyngeal epithelium1.44e-086
throat7.61e-072


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)
MA0003.10.00512623
MA0004.10.711841
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.00275422
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.11.2891
MA0038.10.34128
MA0040.11.44943
MA0041.10.27117
MA0042.10.687159
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.120131
MA0056.10
MA0057.10.219783
MA0058.11.03067
MA0059.11.02688
MA0060.10.0671843
MA0061.10.0537738
MA0063.10
MA0066.10.905108
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.098235
MA0074.10.894848
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.10.205547
MA0091.11.32108
MA0092.10.228476
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.10.930697
MA0101.10.141917
MA0103.10.411001
MA0105.10.0162551
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.617603
MA0113.10.39123
MA0114.10.30732
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.917713
MA0139.10.0481205
MA0140.11.49639
MA0141.10.180729
MA0142.11.2271
MA0143.11.01483
MA0144.10.284854
MA0145.10.278475
MA0146.10.00187713
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.20.425026
MA0035.21.49427
MA0039.20.0182366
MA0138.20.425279
MA0002.20.480166
MA0137.20.465392
MA0104.20.236755
MA0047.20.366327
MA0112.20.124752
MA0065.20.287056
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.0723831
MA0155.10.0077078
MA0156.10.91467
MA0157.11.17385
MA0158.10
MA0159.10.327637
MA0160.10.288813
MA0161.10
MA0162.10.0065085
MA0163.10.0031263
MA0164.10.402162
MA0080.20.851709
MA0018.20.378086
MA0099.20.312108
MA0079.20.00441516
MA0102.21.1957
MA0258.10.27007
MA0259.10.340204
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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