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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:03, 17 September 2013


Full id: C239_CD4_lymphangiectasia_CD8_NK_mycosis_Renal_hairy



Phase1 CAGE Peaks

Hg19::chr11:133815219..133815230,-p@chr11:133815219..133815230
-
Hg19::chr11:133815282..133815297,-p@chr11:133815282..133815297
-
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
-
Hg19::chr14:100533978..100533994,+p@chr14:100533978..100533994
+
Hg19::chr14:23008000..23008038,+p1@TRAJ6
Hg19::chr14:91708423..91708436,-p@chr14:91708423..91708436
-
Hg19::chr14:91709954..91709967,-p@chr14:91709954..91709967
-
Hg19::chr14:91709994..91710001,-p@chr14:91709994..91710001
-
Hg19::chr14:91710043..91710078,-p@chr14:91710043..91710078
-
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
-
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)
MA0003.10.0404189
MA0004.10.0206186
MA0006.10.425117
MA0007.10.0789137
MA0009.10.222068
MA0014.10.0285067
MA0017.10.351449
MA0019.10.216967
MA0024.10.157836
MA0025.10.315513
MA0027.11.68322
MA0028.10.0713574
MA0029.10.16898
MA0030.10.16233
MA0031.10.1271
MA0038.10.0453214
MA0040.10.98812
MA0041.10.10363
MA0042.10.402991
MA0043.10.222275
MA0046.11.15685
MA0048.10.428062
MA0050.11.78652
MA0051.11.0541
MA0052.10.17471
MA0055.10.0835973
MA0056.10
MA0057.10.51881
MA0058.10.0397438
MA0059.10.00745523
MA0060.10.000270366
MA0061.10.695896
MA0063.10
MA0066.10.173138
MA0067.10.460571
MA0068.10.321704
MA0069.10.212494
MA0070.10.592644
MA0071.10.589458
MA0072.10.202487
MA0073.16.93842
MA0074.10.381591
MA0076.10.267221
MA0077.10.197639
MA0078.10.271002
MA0081.10.41442
MA0083.10.643872
MA0084.10.621693
MA0087.10.200944
MA0088.10.179385
MA0089.10
MA0090.10.767429
MA0091.13.47637
MA0092.10.355672
MA0093.10.00322942
MA0095.10
MA0098.10
MA0100.10.185831
MA0101.10.663892
MA0103.11.12543
MA0105.10.149865
MA0106.13.51804
MA0107.11.01315
MA0108.20.125525
MA0109.10
MA0111.11.96016
MA0113.10.0644728
MA0114.11.25314
MA0115.10.398428
MA0116.10.566741
MA0117.10.690984
MA0119.11.90382
MA0122.10.26509
MA0124.10.365763
MA0125.10.302328
MA0130.10
MA0131.10.291964
MA0132.10
MA0133.10
MA0135.10.242288
MA0136.11.54842
MA0139.10.0126515
MA0140.10.582599
MA0141.10.409287
MA0142.10.111215
MA0143.10.0645373
MA0144.10.654133
MA0145.10.68656
MA0146.10.0362348
MA0147.10.00736283
MA0148.10.0255324
MA0149.11.27206
MA0062.20.486452
MA0035.20.0337499
MA0039.20.606232
MA0138.20.0793656
MA0002.20.605809
MA0137.20.169735
MA0104.20.00223039
MA0047.20.200722
MA0112.20.20225
MA0065.20.448805
MA0150.10.283418
MA0151.10
MA0152.10.0356056
MA0153.10.29008
MA0154.10.404382
MA0155.10.837437
MA0156.11.3553
MA0157.10.0983533
MA0158.10
MA0159.11.06763
MA0160.10.842542
MA0161.10
MA0162.10.0189675
MA0163.12.02331
MA0164.10.243379
MA0080.22.76701
MA0018.20.0591151
MA0099.20.942513
MA0079.20.0168689
MA0102.20.6549
MA0258.10.423604
MA0259.10.156825
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

(#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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