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Coexpression cluster:C239

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Full id: C239_CD4_lymphangiectasia_CD8_NK_mycosis_Renal_hairy



Phase1 CAGE Peaks

Hg19::chr11:133815219..133815230,-p@chr11:133815219..133815230
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Hg19::chr11:133815282..133815297,-p@chr11:133815282..133815297
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Hg19::chr11:67207655..67207691,-p2@CORO1B
Hg19::chr11:67207696..67207709,-p5@CORO1B
Hg19::chr13:113840599..113840624,-p5@PCID2
Hg19::chr13:99121398..99121404,-p@chr13:99121398..99121404
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Hg19::chr14:100533978..100533994,+p@chr14:100533978..100533994
+
Hg19::chr14:23008000..23008038,+p1@TRAJ6
Hg19::chr14:91708423..91708436,-p@chr14:91708423..91708436
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Hg19::chr14:91709954..91709967,-p@chr14:91709954..91709967
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Hg19::chr14:91709994..91710001,-p@chr14:91709994..91710001
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Hg19::chr14:91710043..91710078,-p@chr14:91710043..91710078
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Hg19::chr14:91710858..91710893,-p2@GPR68
Hg19::chr14:91710916..91710929,-p4@GPR68
Hg19::chr16:30194118..30194165,+p@chr16:30194118..30194165
+
Hg19::chr16:30197413..30197437,+p2@CORO1A
Hg19::chr16:3115626..3115648,+p1@IL32
Hg19::chr16:3117545..3117588,+p8@IL32
Hg19::chr16:3117688..3117736,+p7@IL32
Hg19::chr16:3118178..3118198,+p6@IL32
Hg19::chr16:3118203..3118241,-p@chr16:3118203..3118241
-
Hg19::chr16:3119238..3119248,+p@chr16:3119238..3119248
+
Hg19::chr16:3119304..3119330,-p@chr16:3119304..3119330
-
Hg19::chr16:31271243..31271270,+p3@ITGAM
Hg19::chr17:17082907..17082918,+p@chr17:17082907..17082918
+
Hg19::chr17:4844362..4844368,+p@chr17:4844362..4844368
+
Hg19::chr17:78865999..78866032,-p@chr17:78865999..78866032
-
Hg19::chr18:60867334..60867342,-p@chr18:60867334..60867342
-
Hg19::chr18:67614645..67614674,-p2@CD226
Hg19::chr19:14143080..14143099,+p@chr19:14143080..14143099
+
Hg19::chr19:14143101..14143121,+p@chr19:14143101..14143121
+
Hg19::chr19:30205532..30205579,-p@chr19:30205532..30205579
-
Hg19::chr19:41808608..41808626,+p33@HNRNPUL1
Hg19::chr19:41808637..41808666,+p25@HNRNPUL1
Hg19::chr22:39493207..39493223,+p3@APOBEC3H
Hg19::chr22:39493235..39493261,+p2@APOBEC3H
Hg19::chr22:39493268..39493317,+p1@APOBEC3H
Hg19::chr22:50908325..50908344,-p@chr22:50908325..50908344
-
Hg19::chr22:50908348..50908373,-p@chr22:50908348..50908373
-
Hg19::chr2:26017511..26017565,-p@chr2:26017511..26017565
-
Hg19::chr3:150920950..150920962,-p2@GPR171
Hg19::chr3:150920988..150921009,-p1@GPR171
Hg19::chr3:151961403..151961428,+p7@MBNL1
Hg19::chr3:48520793..48520806,-p20@SHISA5
Hg19::chr3:48520822..48520833,-p17@SHISA5
Hg19::chr3:48520846..48520874,-p12@SHISA5
Hg19::chr3:48520879..48520892,-p18@SHISA5
Hg19::chr4:90228185..90228196,-p@chr4:90228185..90228196
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Hg19::chr7:150691829..150691867,+p@chr7:150691829..150691867
+
Hg19::chr8:8777580..8777590,+p@chr8:8777580..8777590
+
Hg19::chr8:8777601..8777633,+p@chr8:8777601..8777633
+
Hg19::chr9:132631644..132631655,+p@chr9:132631644..132631655
+
Hg19::chr9:139001620..139001639,+p@chr9:139001620..139001639
+
Hg19::chr9:139001642..139001662,+p@chr9:139001642..139001662
+
Hg19::chr9:139869497..139869510,+p12@PTGDS
Hg19::chr9:139869524..139869539,+p7@PTGDS
Hg19::chr9:34647078..34647100,+p4@GALT


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:0022410circadian sleep/wake cycle process0.0164252914164606
GO:0045187regulation of circadian sleep/wake cycle, sleep0.0164252914164606
GO:0042749regulation of circadian sleep/wake cycle0.0164252914164606
GO:0050802circadian sleep/wake cycle, sleep0.0164252914164606
GO:0004667prostaglandin-D synthase activity0.0197039680044342
GO:0042745circadian sleep/wake cycle0.0197039680044342
GO:0048512circadian behavior0.0197039680044342
GO:0008108UDP-glucose:hexose-1-phosphate uridylyltransferase activity0.0197039680044342
GO:0042752regulation of circadian rhythm0.0197039680044342
GO:0007622rhythmic behavior0.0197039680044342
GO:0030431sleep0.0298448315359082
GO:0001948glycoprotein binding0.032824000262067
GO:0046457prostanoid biosynthetic process0.0468610756854441
GO:0001516prostaglandin biosynthetic process0.0468610756854441
GO:0022610biological adhesion0.0475287231674542
GO:0007155cell adhesion0.0475287231674542



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 cell8.12e-4518
alpha-beta T cell8.12e-4518
immature T cell8.12e-4518
mature T cell8.12e-4518
immature alpha-beta T cell8.12e-4518
T cell8.11e-4225
pro-T cell8.11e-4225
lymphoid lineage restricted progenitor cell4.10e-3452
lymphocyte2.61e-3353
common lymphoid progenitor2.61e-3353
nucleate cell8.66e-3255
CD8-positive, alpha-beta T cell2.40e-2811
leukocyte8.95e-18136
nongranular leukocyte1.60e-17115
CD4-positive, alpha-beta T cell9.58e-166
hematopoietic lineage restricted progenitor cell5.18e-13120
hematopoietic stem cell1.73e-12168
angioblastic mesenchymal cell1.73e-12168
hematopoietic cell2.32e-11177
hematopoietic oligopotent progenitor cell9.49e-11161
hematopoietic multipotent progenitor cell9.49e-11161
naive T cell6.46e-093
natural killer cell8.18e-093
pro-NK cell8.18e-093
single nucleate cell3.17e-083
mononuclear cell3.17e-083
basophil4.49e-083
Uber Anatomy
Ontology termp-valuen
blood1.41e-1815
haemolymphatic fluid1.41e-1815
organism substance1.41e-1815
hemopoietic organ3.72e-127
immune organ3.72e-127
thymus2.21e-104
hemolymphoid system gland2.21e-104
thymic region2.21e-104
pharyngeal gland2.21e-104
thymus primordium2.21e-104
pharyngeal epithelium6.54e-076


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)

{{{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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#1053872.991308992037290.008586504343841030.0327131626296434
BCL11A#53335104.977097386597732.78366640123425e-050.000588389668647042
EBF1#1879162.500060869212350.0003962662416706530.00387433533175822
EGR1#1958191.662726364936710.01292238757581010.046457873873667
MEF2A#4205103.288286124498960.0007986423313743190.00616887851833463
TCF12#6938122.238834716249770.006045714118167830.0270897690401291



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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