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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:11, 17 September 2013


Full id: C276_mesothelioma_kidney_renal_small_clear_cerebellum_Renal



Phase1 CAGE Peaks

Hg19::chr10:34987954..34987974,-p@chr10:34987954..34987974
-
Hg19::chr10:35013710..35013742,+p@chr10:35013710..35013742
+
Hg19::chr12:127690461..127690477,-p@chr12:127690461..127690477
-
Hg19::chr16:12071528..12071579,-p@chr16:12071528..12071579
-
Hg19::chr16:12071607..12071614,-p@chr16:12071607..12071614
-
Hg19::chr16:12071625..12071637,-p@chr16:12071625..12071637
-
Hg19::chr16:12071655..12071667,-p@chr16:12071655..12071667
-
Hg19::chr17:68130483..68130490,+p@chr17:68130483..68130490
+
Hg19::chr18:8707570..8707590,-p@chr18:8707570..8707590
-
Hg19::chr18:8707629..8707682,-p@chr18:8707629..8707682
-
Hg19::chr19:21907110..21907113,+p@chr19:21907110..21907113
+
Hg19::chr1:145727608..145727615,+p13@PDZK1
Hg19::chr1:145727640..145727651,+p5@PDZK1
Hg19::chr1:201178082..201178093,+p@chr1:201178082..201178093
+
Hg19::chr1:51796987..51797001,-p8@TTC39A
Hg19::chr1:62212760..62212775,+p@chr1:62212760..62212775
+
Hg19::chr1:81001373..81001388,+p2@ENST00000418041
p2@ENST00000443104
Hg19::chr1:81001398..81001426,+p1@ENST00000418041
p1@ENST00000443104
Hg19::chr1:858638..858648,+p@chr1:858638..858648
+
Hg19::chr1:874109..874143,+p@chr1:874109..874143
+
Hg19::chr1:874201..874212,+p8@SAMD11
Hg19::chr22:35779090..35779122,+p9@HMOX1
Hg19::chr22:45072983..45072995,+p9@PRR5
Hg19::chr2:191792376..191792426,+p3@GLS
Hg19::chr2:234526272..234526280,+p2@UGT1A8
Hg19::chr2:234526341..234526346,+p1@UGT1A8
Hg19::chr3:19962031..19962047,-p@chr3:19962031..19962047
-
Hg19::chr3:69812649..69812658,+p20@MITF
Hg19::chr3:69812701..69812729,+p9@MITF
Hg19::chr3:69812731..69812742,+p19@MITF
Hg19::chr3:69812745..69812760,+p10@MITF
Hg19::chr3:69812764..69812775,+p18@MITF
Hg19::chr3:69812798..69812824,+p8@MITF
Hg19::chr3:69812852..69812864,+p17@MITF
Hg19::chr3:69812877..69812886,+p22@MITF
Hg19::chr4:160521424..160521437,-p@chr4:160521424..160521437
-
Hg19::chr4:23735183..23735192,-p1@ENST00000507666
Hg19::chr5:13903866..13903886,-p@chr5:13903866..13903886
-
Hg19::chr5:156485016..156485034,-p3@HAVCR1
Hg19::chr5:168246378..168246386,+p@chr5:168246378..168246386
+
Hg19::chr5:58806588..58806600,-p@chr5:58806588..58806600
-
Hg19::chr7:107968921..107968937,-p9@NRCAM
Hg19::chr7:107968952..107968990,-p5@NRCAM
Hg19::chr7:107968999..107969017,-p10@NRCAM
Hg19::chr9:119741711..119741743,-p@chr9:119741711..119741743
-
Hg19::chrX:146262612..146262636,+p@chrX:146262612..146262636
+
Hg19::chrX:41449223..41449229,-p20@CASK


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:0043301negative regulation of leukocyte degranulation0.019335975245152
GO:0006543glutamine catabolic process0.019335975245152
GO:0045920negative regulation of exocytosis0.019335975245152
GO:0043305negative regulation of mast cell degranulation0.019335975245152
GO:0005124scavenger receptor binding0.019335975245152
GO:0032764negative regulation of mast cell cytokine production0.019335975245152
GO:0004392heme oxygenase (decyclizing) activity0.019335975245152
GO:0031670cellular response to nutrient0.019335975245152
GO:0006788heme oxidation0.019335975245152
GO:0045162clustering of voltage-gated sodium channels0.019335975245152
GO:0002701negative regulation of production of molecular mediator of immune response0.019335975245152
GO:0045666positive regulation of neuron differentiation0.019335975245152
GO:0042167heme catabolic process0.019335975245152
GO:0046149pigment catabolic process0.019335975245152
GO:0002719negative regulation of cytokine production during immune response0.019335975245152
GO:0005792microsome0.019335975245152
GO:0042598vesicular fraction0.019335975245152
GO:0032762mast cell cytokine production0.019335975245152
GO:0032763regulation of mast cell cytokine production0.019335975245152
GO:0043304regulation of mast cell degranulation0.019335975245152
GO:0002698negative regulation of immune effector process0.019335975245152
GO:0043300regulation of leukocyte degranulation0.0195193122881176
GO:0045161neuronal ion channel clustering0.0195193122881176
GO:0007413axonal fasciculation0.0195193122881176
GO:0006787porphyrin catabolic process0.0195193122881176
GO:0033015tetrapyrrole catabolic process0.0195193122881176
GO:0004359glutaminase activity0.0202973959740903
GO:0004630phospholipase D activity0.0202973959740903
GO:0030506ankyrin binding0.0202973959740903
GO:0043392negative regulation of DNA binding0.0202973959740903
GO:0043303mast cell degranulation0.021360020662496
GO:0002448mast cell mediated immunity0.021360020662496
GO:0051100negative regulation of binding0.021360020662496
GO:0045576mast cell activation0.021360020662496
GO:0043299leukocyte degranulation0.021360020662496
GO:0030318melanocyte differentiation0.021360020662496
GO:0045768positive regulation of anti-apoptosis0.021360020662496
GO:0050931pigment cell differentiation0.021360020662496
GO:0002718regulation of cytokine production during immune response0.0217385700965078
GO:0002700regulation of production of molecular mediator of immune response0.0217385700965078
GO:0002367cytokine production during immune response0.0217385700965078
GO:0002444myeloid leukocyte mediated immunity0.0217385700965078
GO:0002683negative regulation of immune system process0.0220507010573156
GO:0001818negative regulation of cytokine production0.0220507010573156
GO:0031669cellular response to nutrient levels0.0220507010573156
GO:0042551neuron maturation0.0220507010573156
GO:0051101regulation of DNA binding0.022767708270412
GO:0008038neuron recognition0.022767708270412
GO:0004385guanylate kinase activity0.022767708270412
GO:0045767regulation of anti-apoptosis0.02386032000429
GO:0030516regulation of axon extension0.02386032000429
GO:0031668cellular response to extracellular stimulus0.0272944817406109
GO:0002697regulation of immune effector process0.0281572440458984
GO:0017157regulation of exocytosis0.0281572440458984
GO:0048066pigmentation during development0.0289579016086571
GO:0043433negative regulation of transcription factor activity0.0289579016086571
GO:0015893drug transport0.0297028791663547
GO:0048675axon extension0.0297028791663547
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.0326260269476884
GO:0009065glutamine family amino acid catabolic process0.0326770919232935
GO:0030165PDZ domain binding0.0326770919232935
GO:0042168heme metabolic process0.0326770919232935
GO:0043627response to estrogen stimulus0.0353648820613477
GO:0051716cellular response to stimulus0.037595458508835
GO:0006541glutamine metabolic process0.037595458508835
GO:0051241negative regulation of multicellular organismal process0.037595458508835
GO:0007416synaptogenesis0.037595458508835
GO:0050770regulation of axonogenesis0.037595458508835
GO:0016599caveolar membrane0.037595458508835
GO:0045664regulation of neuron differentiation0.037595458508835
GO:0002440production of molecular mediator of immune response0.0379519283882688
GO:0002274myeloid leukocyte activation0.0379519283882688
GO:0051098regulation of binding0.0388132719405581
GO:0005901caveola0.0396509746626627
GO:0006778porphyrin metabolic process0.0404659822718011
GO:0051051negative regulation of transport0.041259190710588
GO:0015020glucuronosyltransferase activity0.0446465934736366
GO:0033013tetrapyrrole metabolic process0.0453644961172646
GO:0001764neuron migration0.0454880875821726
GO:0008629induction of apoptosis by intracellular signals0.0454880875821726
GO:0048545response to steroid hormone stimulus0.0457166616648321
GO:0050767regulation of neurogenesis0.0457166616648321
GO:0008037cell recognition0.0457166616648321
GO:0019201nucleotide kinase activity0.0457166616648321
GO:0050808synapse organization and biogenesis0.0463615983090679
GO:0001817regulation of cytokine production0.0477366896370438
GO:0007584response to nutrient0.0477366896370438
GO:0042440pigment metabolic process0.0477366896370438
GO:0042221response to chemical stimulus0.0477366896370438
GO:0042770DNA damage response, signal transduction0.0482512708214898
GO:0048469cell maturation0.0499274040431469



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
kidney3.38e-1226
kidney mesenchyme3.38e-1226
upper urinary tract3.38e-1226
kidney rudiment3.38e-1226
kidney field3.38e-1226
cavitated compound organ2.36e-1031
urinary system structure4.59e-0747
renal system6.25e-0748
Disease
Ontology termp-valuen
clear cell adenocarcinoma9.07e-182


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)
MA0003.12.6016e-09
MA0004.10.0359622
MA0006.10.0388776
MA0007.10.0311376
MA0009.10.275766
MA0014.11.67622e-07
MA0017.10.528773
MA0019.12.74329
MA0024.11.11554
MA0025.10.376628
MA0027.11.7662
MA0028.10.00904529
MA0029.10.620121
MA0030.10.602396
MA0031.10.97517
MA0038.10.245663
MA0040.10.629226
MA0041.10.159732
MA0042.10.131646
MA0043.10.275993
MA0046.17.96925
MA0048.10.134218
MA0050.10.311918
MA0051.10.517329
MA0052.10.223346
MA0055.11.00732
MA0056.10
MA0057.10.193206
MA0058.10.0155786
MA0059.10.0713951
MA0060.10.0260418
MA0061.10.0159627
MA0063.10
MA0066.10.0700626
MA0067.10.529198
MA0068.11.25405
MA0069.10.265257
MA0070.10.257372
MA0071.10.0556134
MA0072.10.254227
MA0073.12.51468e-07
MA0074.10.51581
MA0076.10.0182587
MA0077.10.248866
MA0078.10.112125
MA0081.10.605762
MA0083.10.281174
MA0084.10.695499
MA0087.10.703294
MA0088.10.309078
MA0089.10
MA0090.11.04726
MA0091.10.610215
MA0092.10.511154
MA0093.10.00767494
MA0095.10
MA0098.10
MA0100.10.55433
MA0101.10.246389
MA0103.10.385713
MA0105.10.0102156
MA0106.10.0870163
MA0107.10.016496
MA0108.20.167426
MA0109.10
MA0111.10.249833
MA0113.10.647283
MA0114.10.380011
MA0115.10.464275
MA0116.10.0173612
MA0117.10.303182
MA0119.10.0620298
MA0122.10.862493
MA0124.10.429905
MA0125.11.69526
MA0130.10
MA0131.10.771155
MA0132.10
MA0133.10
MA0135.10.297838
MA0136.10.0726858
MA0139.10.0354674
MA0140.10.44418
MA0141.10.897917
MA0142.10.150759
MA0143.10.647667
MA0144.10.334737
MA0145.10.1252
MA0146.10.000209428
MA0147.10.00300228
MA0148.10.671391
MA0149.10.0514353
MA0062.20.000448472
MA0035.20.44283
MA0039.21.54635e-05
MA0138.20.362512
MA0002.20.717689
MA0137.20.0491622
MA0104.20.00097131
MA0047.20.279106
MA0112.20.0350613
MA0065.20.686143
MA0150.13.40491
MA0151.10
MA0152.10.456823
MA0153.12.49225
MA0154.10.0228192
MA0155.10.000129408
MA0156.10.0502819
MA0157.10.833758
MA0158.10
MA0159.10.256716
MA0160.10.180181
MA0161.10
MA0162.13.45044e-08
MA0163.18.60419e-05
MA0164.10.100116
MA0080.20.114527
MA0018.20.0876241
MA0099.21.69472
MA0079.20
MA0102.20.729507
MA0258.10.178137
MA0259.10.0649546
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
NR3C1#2908123.822899573916524.49857387869627e-050.000791620147122425



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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