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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:02, 17 September 2013


Full id: C235_Intestinal_Prostate_liver_colon_small_kidney_pancreas



Phase1 CAGE Peaks

Hg19::chr10:1568835..1568845,+p1@ADARB2-AS1
Hg19::chr10:82264452..82264468,+p@chr10:82264452..82264468
+
Hg19::chr10:82264474..82264504,+p@chr10:82264474..82264504
+
Hg19::chr12:24768892..24768895,-p@chr12:24768892..24768895
-
Hg19::chr12:93516455..93516485,-p@chr12:93516455..93516485
-
Hg19::chr13:42179544..42179550,-p@chr13:42179544..42179550
-
Hg19::chr13:92756353..92756364,+p@chr13:92756353..92756364
+
Hg19::chr13:92756378..92756395,+p@chr13:92756378..92756395
+
Hg19::chr13:92756423..92756437,+p@chr13:92756423..92756437
+
Hg19::chr13:95801212..95801217,-p@chr13:95801212..95801217
-
Hg19::chr16:64527759..64527763,-p@chr16:64527759..64527763
-
Hg19::chr17:48764987..48765013,+p8@ABCC3
Hg19::chr17:48765019..48765037,+p7@ABCC3
Hg19::chr17:79990087..79990104,+p@chr17:79990087..79990104
+
Hg19::chr19:38422775..38422794,+p6@SIPA1L3
Hg19::chr19:41698927..41698955,+p4@CYP2S1
Hg19::chr19:49130770..49130779,+p@chr19:49130770..49130779
+
Hg19::chr19:49130799..49130812,+p@chr19:49130799..49130812
+
Hg19::chr19:953515..953565,+p@chr19:953515..953565
+
Hg19::chr1:246020583..246020602,-p@chr1:246020583..246020602
-
Hg19::chr1:6420713..6420725,-p16@ACOT7
Hg19::chr1:6420737..6420779,-p9@ACOT7
Hg19::chr20:17691468..17691474,-p@chr20:17691468..17691474
-
Hg19::chr21:45670791..45670804,-p@chr21:45670791..45670804
-
Hg19::chr21:45670812..45670824,-p@chr21:45670812..45670824
-
Hg19::chr21:45671014..45671052,-p@chr21:45671014..45671052
-
Hg19::chr2:108931987..108932010,-p@chr2:108931987..108932010
-
Hg19::chr2:165550868..165550878,-p31@COBLL1
Hg19::chr2:205409703..205409714,+p@chr2:205409703..205409714
+
Hg19::chr2:28340361..28340371,+p@chr2:28340361..28340371
+
Hg19::chr2:43022486..43022490,+p@chr2:43022486..43022490
+
Hg19::chr2:43616324..43616335,-p@chr2:43616324..43616335
-
Hg19::chr2:43616357..43616368,-p@chr2:43616357..43616368
-
Hg19::chr3:149388664..149388677,-p35@WWTR1
Hg19::chr3:149388682..149388700,-p31@WWTR1
Hg19::chr3:153375946..153375968,-p@chr3:153375946..153375968
-
Hg19::chr3:47484661..47484686,-p4@SCAP
Hg19::chr3:99796216..99796219,-p@chr3:99796216..99796219
-
Hg19::chr4:121930371..121930408,+p@chr4:121930371..121930408
+
Hg19::chr4:140048091..140048100,-p@chr4:140048091..140048100
-
Hg19::chr4:140048110..140048120,-p@chr4:140048110..140048120
-
Hg19::chr4:69774211..69774248,+p@chr4:69774211..69774248
+
Hg19::chr4:69775342..69775385,+p@chr4:69775342..69775385
+
Hg19::chr4:7168121..7168126,+p@chr4:7168121..7168126
+
Hg19::chr4:74257875..74257904,+p@chr4:74257875..74257904
+
Hg19::chr5:90195083..90195098,+p6@GPR98
Hg19::chr6:22919616..22919625,-p@chr6:22919616..22919625
-
Hg19::chr6:52616408..52616458,-p@chr6:52616408..52616458
-
Hg19::chr6:52617751..52617757,-p@chr6:52617751..52617757
-
Hg19::chr6:52628271..52628275,-p1@GSTA2
Hg19::chr6:84141528..84141537,-p@chr6:84141528..84141537
-
Hg19::chr7:115608319..115608352,-p4@TFEC
Hg19::chr7:115608357..115608372,-p3@TFEC
Hg19::chr7:137749883..137749887,+p@chr7:137749883..137749887
+
Hg19::chr7:142940347..142940351,+p@chr7:142940347..142940351
+
Hg19::chr7:83779919..83779933,-p@chr7:83779919..83779933
-
Hg19::chr8:119760950..119760956,-p@chr8:119760950..119760956
-
Hg19::chr9:138591077..138591111,-p@chr9:138591077..138591111
-
Hg19::chr9:138591319..138591340,-p1@SOHLH1
Hg19::chrX:42850716..42850719,+p@chrX:42850716..42850719
+


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:0045596negative regulation of cell differentiation0.00952990698222064
GO:0051093negative regulation of developmental process0.00952990698222064
GO:0045599negative regulation of fat cell differentiation0.00952990698222064
GO:0006994sterol depletion response, SREBP target gene transcriptional activation0.00952990698222064
GO:0045714regulation of low-density lipoprotein receptor biosynthetic process0.00952990698222064
GO:0045713low-density lipoprotein receptor biosynthetic process0.00952990698222064
GO:0032800receptor biosynthetic process0.00952990698222064
GO:0045716positive regulation of low-density lipoprotein receptor biosynthetic process0.00952990698222064
GO:0003714transcription corepressor activity0.0117275625775505
GO:0030967ER-nuclear sterol response pathway0.0117275625775505
GO:0035104positive regulation of sterol regulatory element binding protein target gene transcription0.0117275625775505
GO:0045939negative regulation of steroid metabolic process0.0117275625775505
GO:0045541negative regulation of cholesterol biosynthetic process0.0117275625775505
GO:0045595regulation of cell differentiation0.0134504222181111
GO:0032799low-density lipoprotein receptor metabolic process0.0134504222181111
GO:0032933SREBP-mediated signaling pathway0.0134504222181111
GO:0006991response to sterol depletion0.0134504222181111
GO:0051055negative regulation of lipid biosynthetic process0.0145159930101286
GO:0045598regulation of fat cell differentiation0.0145159930101286
GO:0045540regulation of cholesterol biosynthetic process0.0145159930101286
GO:0048496maintenance of organ identity0.0145159930101286
GO:0003713transcription coactivator activity0.0155094644082816
GO:0050810regulation of steroid biosynthetic process0.0165649715120584
GO:0016564transcription repressor activity0.018285306286224
GO:0045833negative regulation of lipid metabolic process0.018285306286224
GO:0045893positive regulation of transcription, DNA-dependent0.0185734867977686
GO:0050793regulation of developmental process0.0199957697093771
GO:0046890regulation of lipid biosynthetic process0.0210120263228671
GO:0016290palmitoyl-CoA hydrolase activity0.0210120263228671
GO:0050794regulation of cellular process0.0218608434207864
GO:0045941positive regulation of transcription0.0223965944072342
GO:0019218regulation of steroid metabolic process0.0223965944072342
GO:0008514organic anion transmembrane transporter activity0.0223965944072342
GO:0043193positive regulation of gene-specific transcription0.0223965944072342
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0229576873497736
GO:0043112receptor metabolic process0.0232644915990176
GO:0003712transcription cofactor activity0.0234847394853598
GO:0032583regulation of gene-specific transcription0.0234847394853598
GO:0016563transcription activator activity0.0234847394853598
GO:0050789regulation of biological process0.0237586302636781
GO:0048523negative regulation of cellular process0.0237586302636781
GO:0048519negative regulation of biological process0.0258764488009861
GO:0045494photoreceptor cell maintenance0.0265458183502484
GO:0045444fat cell differentiation0.0276683402458473
GO:0031325positive regulation of cellular metabolic process0.0281644629784744
GO:0031324negative regulation of cellular metabolic process0.0299487413081397
GO:0009893positive regulation of metabolic process0.0308239919572163
GO:0000062acyl-CoA binding0.0313095896085146
GO:0065007biological regulation0.0313095896085146
GO:0016291acyl-CoA thioesterase activity0.0313095896085146
GO:0006984ER-nuclear signaling pathway0.0313095896085146
GO:0005622intracellular0.0331326485388953
GO:0008134transcription factor binding0.0331326485388953
GO:0009892negative regulation of metabolic process0.0331326485388953
GO:0006695cholesterol biosynthetic process0.033485908266528
GO:0001649osteoblast differentiation0.033485908266528
GO:0005789endoplasmic reticulum membrane0.033485908266528
GO:0050381unspecific monooxygenase activity0.033485908266528
GO:0016289CoA hydrolase activity0.033485908266528
GO:0042175nuclear envelope-endoplasmic reticulum network0.0340494306404601
GO:0019216regulation of lipid metabolic process0.0348701607308212
GO:0044424intracellular part0.0368808265656214
GO:0005504fatty acid binding0.0373658113617306
GO:0016126sterol biosynthetic process0.0386543135008576
GO:0044432endoplasmic reticulum part0.0386543135008576
GO:0005737cytoplasm0.0409718545142063
GO:0004364glutathione transferase activity0.0497833226662805



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>


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)
MA0003.13.78469e-05
MA0004.10.392783
MA0006.10.117103
MA0007.10.883766
MA0009.11.77356
MA0014.16.58983e-05
MA0017.12.53451
MA0019.10.0534661
MA0024.10.146446
MA0025.10.299942
MA0027.11.66118
MA0028.10.00306998
MA0029.12.83878
MA0030.10.898568
MA0031.10.373498
MA0038.10.357559
MA0040.10.160513
MA0041.11.04134
MA0042.10.605322
MA0043.10.208842
MA0046.15.98423
MA0048.10.00805118
MA0050.10.0719202
MA0051.10.0387309
MA0052.10.162725
MA0055.10.00144813
MA0056.10
MA0057.10.00659259
MA0058.10.851431
MA0059.10.207159
MA0060.10.00161032
MA0061.10.0665977
MA0063.10
MA0066.10.358282
MA0067.10.442801
MA0068.10.00455052
MA0069.11.09581
MA0070.10.192383
MA0071.12.71318
MA0072.10.554995
MA0073.10.164812
MA0074.10.15136
MA0076.10.00746275
MA0077.10.543642
MA0078.10.0711369
MA0081.10.846163
MA0083.10.213446
MA0084.10.602392
MA0087.11.05139
MA0088.10.355765
MA0089.10
MA0090.11.34213
MA0091.10.972938
MA0092.10.0123367
MA0093.10.581594
MA0095.10
MA0098.10
MA0100.10.043811
MA0101.10.124918
MA0103.11.0226
MA0105.10.0716143
MA0106.10.430165
MA0107.10.109498
MA0108.20.744857
MA0109.10
MA0111.10.140961
MA0113.11.70263
MA0114.11.73707
MA0115.10.993103
MA0116.10.114371
MA0117.10.233123
MA0119.10.181734
MA0122.10.250579
MA0124.10.349309
MA0125.10.287016
MA0130.10
MA0131.10.0782661
MA0132.10
MA0133.10
MA0135.10.646969
MA0136.10.369589
MA0139.10.00918816
MA0140.12.15676
MA0141.12.30899
MA0142.11.12972
MA0143.10.800367
MA0144.10.0844908
MA0145.10.183165
MA0146.10.0466923
MA0147.10.119405
MA0148.14.12801
MA0149.10.0272934
MA0062.20.00324441
MA0035.21.22797
MA0039.20.00077015
MA0138.20.0716075
MA0002.20.708765
MA0137.20.146163
MA0104.20.18006
MA0047.22.64465
MA0112.20.0402889
MA0065.20.473537
MA0150.10.120624
MA0151.10
MA0152.10.126738
MA0153.14.83538
MA0154.10.330225
MA0155.10.448794
MA0156.10.149291
MA0157.10.300508
MA0158.10
MA0159.10.34844
MA0160.12.0147
MA0161.10
MA0162.10.00159699
MA0163.10.596508
MA0164.11.26557
MA0080.20.231037
MA0018.20.195137
MA0099.20.301237
MA0079.24.37304e-07
MA0102.20.635361
MA0258.10.721161
MA0259.10.0243485
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
FOXA1#3169152.770354937346360.000221210271264380.00249573074652486
FOXA2#317083.28406183368870.002860868956847130.0155060611855393
HNF4A#317293.469843554443050.001051820627832720.00743342093315887
HNF4G#317483.833789670192910.001087032709936060.00760049602952478



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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