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Coexpression cluster:C191: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:52, 17 September 2013


Full id: C191_leiomyoblastoma_Mast_parietal_acute_bone_neuroepithelioma_embryonic



Phase1 CAGE Peaks

Hg19::chr10:119217804..119217808,-p@chr10:119217804..119217808
-
Hg19::chr11:11199184..11199203,+p@chr11:11199184..11199203
+
Hg19::chr11:11204475..11204502,+p@chr11:11204475..11204502
+
Hg19::chr11:11204503..11204513,+p@chr11:11204503..11204513
+
Hg19::chr11:11204661..11204666,+p@chr11:11204661..11204666
+
Hg19::chr11:11204710..11204723,+p@chr11:11204710..11204723
+
Hg19::chr11:11239563..11239568,+p@chr11:11239563..11239568
+
Hg19::chr11:11261470..11261474,+p1@MTND5P21
Hg19::chr11:11267941..11267951,+p@chr11:11267941..11267951
+
Hg19::chr11:11280165..11280169,+p@chr11:11280165..11280169
+
Hg19::chr11:11306477..11306480,+p@chr11:11306477..11306480
+
Hg19::chr12:92402520..92402535,-p@chr12:92402520..92402535
-
Hg19::chr14:102701899..102701936,-p6@MOK
Hg19::chr14:85975105..85975111,-p@chr14:85975105..85975111
-
Hg19::chr14:85982823..85982842,+p@chr14:85982823..85982842
+
Hg19::chr15:47476379..47476409,+p6@SEMA6D
Hg19::chr15:47476835..47476844,-p@chr15:47476835..47476844
-
Hg19::chr15:47476886..47476899,-p@chr15:47476886..47476899
-
Hg19::chr15:95294364..95294378,+p@chr15:95294364..95294378
+
Hg19::chr15:96037007..96037012,-p1@ENST00000554412
Hg19::chr15:96390170..96390194,+p@chr15:96390170..96390194
+
Hg19::chr17:27044011..27044042,-p@chr17:27044011..27044042
-
Hg19::chr17:54711126..54711143,-p@chr17:54711126..54711143
-
Hg19::chr17:54711165..54711172,-p@chr17:54711165..54711172
-
Hg19::chr17:54711180..54711190,-p@chr17:54711180..54711190
-
Hg19::chr18:6683449..6683456,+p@chr18:6683449..6683456
+
Hg19::chr19:46628057..46628066,-p2@IGFL3
Hg19::chr19:49014956..49014973,-p4@AB384647
Hg19::chr1:170283847..170283854,-p@chr1:170283847..170283854
-
Hg19::chr1:170285936..170285978,+p@chr1:170285936..170285978
+
Hg19::chr1:19992392..19992403,+p5@HTR6
Hg19::chr1:26349001..26349015,+p@chr1:26349001..26349015
+
Hg19::chr1:90308844..90308857,+p36@LRRC8D
Hg19::chr20:31647705..31647739,+p@chr20:31647705..31647739
+
Hg19::chr2:196313239..196313248,+p1@ENST00000413290
Hg19::chr2:218290216..218290256,-p@chr2:218290216..218290256
-
Hg19::chr2:234826016..234826024,+p1@TRPM8
Hg19::chr2:234992199..234992202,-p@chr2:234992199..234992202
-
Hg19::chr2:66662797..66662818,+p10@MEIS1
Hg19::chr2:68019731..68019735,-p@chr2:68019731..68019735
-
Hg19::chr2:68054768..68054773,-p@chr2:68054768..68054773
-
Hg19::chr2:68280395..68280440,-p4@C1D
Hg19::chr2:71776374..71776384,+p@chr2:71776374..71776384
+
Hg19::chr2:97572846..97572862,-p@chr2:97572846..97572862
-
Hg19::chr3:30199912..30199921,+p@chr3:30199912..30199921
+
Hg19::chr3:30414583..30414594,+p@chr3:30414583..30414594
+
Hg19::chr3:80101031..80101042,+p@chr3:80101031..80101042
+
Hg19::chr3:85868272..85868282,-p@chr3:85868272..85868282
-
Hg19::chr3:85868324..85868358,-p@chr3:85868324..85868358
-
Hg19::chr4:157997240..157997259,+p2@GLRB
Hg19::chr4:157998021..157998028,-p@chr4:157998021..157998028
-
Hg19::chr4:158186667..158186674,-p@chr4:158186667..158186674
-
Hg19::chr4:168728249..168728254,-p@chr4:168728249..168728254
-
Hg19::chr4:54886472..54886506,+p@chr4:54886472..54886506
+
Hg19::chr5:167089089..167089121,+p@chr5:167089089..167089121
+
Hg19::chr5:23687537..23687541,+p@chr5:23687537..23687541
+
Hg19::chr5:23797853..23797862,-p@chr5:23797853..23797862
-
Hg19::chr5:24083424..24083429,+p@chr5:24083424..24083429
+
Hg19::chr6:133275530..133275540,+p@chr6:133275530..133275540
+
Hg19::chr6:133275544..133275556,+p@chr6:133275544..133275556
+
Hg19::chr6:133275558..133275575,+p@chr6:133275558..133275575
+
Hg19::chr6:133275582..133275585,+p@chr6:133275582..133275585
+
Hg19::chr6:133275614..133275622,+p@chr6:133275614..133275622
+
Hg19::chr6:133294363..133294364,+p@chr6:133294363..133294364
+
Hg19::chr6:33140464..33140471,-p@chr6:33140464..33140471
-
Hg19::chr6:36906253..36906260,-p@chr6:36906253..36906260
-
Hg19::chr6:75462110..75462112,-p@chr6:75462110..75462112
-
Hg19::chr6:91296707..91296721,-p3@MAP3K7
Hg19::chr6:91296737..91296821,-p1@MAP3K7
Hg19::chr6:91405526..91405531,-p@chr6:91405526..91405531
-
Hg19::chr6:91405535..91405543,-p@chr6:91405535..91405543
-
Hg19::chr6:91602280..91602289,+p@chr6:91602280..91602289
+
Hg19::chr6:91705096..91705099,+p@chr6:91705096..91705099
+
Hg19::chr7:16569917..16569927,-p9@SOSTDC1
Hg19::chr7:47648038..47648043,+p@chr7:47648038..47648043
+
Hg19::chr7:47833069..47833071,+p@chr7:47833069..47833071
+
Hg19::chr7:8474731..8474740,+p8@NXPH1
Hg19::chr7:8474792..8474799,+p30@NXPH1
Hg19::chr7:8474804..8474815,+p15@NXPH1
Hg19::chr7:8474817..8474830,+p10@NXPH1
Hg19::chr7:8523611..8523616,+p@chr7:8523611..8523616
+
Hg19::chr8:99264813..99264821,-p18@NIPAL2
Hg19::chr9:3983221..3983226,+p@chr9:3983221..3983226
+
Hg19::chr9:4117869..4117882,-p12@GLIS3
Hg19::chrX:12887946..12887949,-p@chrX:12887946..12887949
-
Hg19::chrX:12964086..12964118,-p@chrX:12964086..12964118
-
Hg19::chrX:25718317..25718324,-p@chrX:25718317..25718324
-
Hg19::chrX:25873187..25873209,+p@chrX:25873187..25873209
+


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:0016594glycine binding0.0377342316088888
GO:0016934extracellular-glycine-gated chloride channel activity0.0377342316088888
GO:0002711positive regulation of T cell mediated immunity0.0377342316088888
GO:0032743positive regulation of interleukin-2 production0.0377342316088888
GO:0002726positive regulation of T cell cytokine production0.0377342316088888
GO:0001964startle response0.0377342316088888
GO:0016933extracellular-glycine-gated ion channel activity0.0377342316088888
GO:0002369T cell cytokine production0.0377342316088888
GO:0002724regulation of T cell cytokine production0.0377342316088888
GO:0002702positive regulation of production of molecular mediator of immune response0.0377342316088888
GO:0002720positive regulation of cytokine production during immune response0.0377342316088888
GO:0002709regulation of T cell mediated immunity0.0377342316088888
GO:0032663regulation of interleukin-2 production0.0377342316088888
GO:0002824positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0377342316088888
GO:0002718regulation of cytokine production during immune response0.0377342316088888
GO:0002821positive regulation of adaptive immune response0.0377342316088888
GO:0002700regulation of production of molecular mediator of immune response0.0377342316088888
GO:0002367cytokine production during immune response0.0377342316088888
GO:0002705positive regulation of leukocyte mediated immunity0.0377342316088888
GO:0002456T cell mediated immunity0.0377342316088888
GO:0002708positive regulation of lymphocyte mediated immunity0.0377342316088888
GO:0002699positive regulation of immune effector process0.0377342316088888
GO:0003702RNA polymerase II transcription factor activity0.0377342316088888
GO:0004969histamine receptor activity0.0377342316088888
GO:0007250activation of NF-kappaB-inducing kinase0.0377342316088888
GO:0002703regulation of leukocyte mediated immunity0.0377342316088888
GO:0002706regulation of lymphocyte mediated immunity0.0377342316088888
GO:0007268synaptic transmission0.0377342316088888
GO:0002819regulation of adaptive immune response0.0377342316088888
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.0377342316088888
GO:0002697regulation of immune effector process0.0421213614924425
GO:0019226transmission of nerve impulse0.0448298461578829
GO:0050852T cell receptor signaling pathway0.0448298461578829
GO:0004709MAP kinase kinase kinase activity0.0460633558676464
GO:0016597amino acid binding0.0493592702435223
GO:0032501multicellular organismal process0.0493592702435223
GO:0032623interleukin-2 production0.0493592702435223



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><br>

Uber Anatomy
Ontology termp-valuen
kidney4.34e-0926
kidney mesenchyme4.34e-0926
upper urinary tract4.34e-0926
kidney rudiment4.34e-0926
kidney field4.34e-0926
cavitated compound organ7.41e-0831


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)
MA0003.13.27121e-06
MA0004.10.0223218
MA0006.10.00179801
MA0007.10.133652
MA0009.10.121077
MA0014.15.44321e-05
MA0017.10.436344
MA0019.10.21324
MA0024.10.554881
MA0025.10.194151
MA0027.11.49708
MA0028.10.0309628
MA0029.10.0830899
MA0030.10.0785674
MA0031.10.204227
MA0038.10.320429
MA0040.10.289272
MA0041.10.329916
MA0042.10.140024
MA0043.10.121231
MA0046.10.370615
MA0048.10.0145201
MA0050.10.141104
MA0051.10.312559
MA0052.10.611982
MA0055.10.0324356
MA0056.10
MA0057.10.25273
MA0058.10.0228085
MA0059.10.0223948
MA0060.10.231704
MA0061.10.217096
MA0063.10
MA0066.11.15244
MA0067.10.317663
MA0068.10.973975
MA0069.10.114002
MA0070.11.72328
MA0071.10.0428908
MA0072.10.106705
MA0073.10.0137447
MA0074.10.311167
MA0076.10.0724478
MA0077.10.337336
MA0078.10.116858
MA0081.10.97886
MA0083.10.124762
MA0084.10.46347
MA0087.10.105589
MA0088.10.0989868
MA0089.10
MA0090.10.901545
MA0091.10.477971
MA0092.11.06968
MA0093.10.00839891
MA0095.10
MA0098.10
MA0100.10.0141875
MA0101.10.32375
MA0103.10.408792
MA0105.10.0610018
MA0106.10.402032
MA0107.10.133193
MA0108.20.444249
MA0109.10
MA0111.10.192229
MA0113.10.436788
MA0114.10.123355
MA0115.10.263593
MA0116.10.140149
MA0117.11.98729
MA0119.10.103678
MA0122.10.467533
MA0124.10.23582
MA0125.10.540113
MA0130.10
MA0131.10.130242
MA0132.10
MA0133.10
MA0135.11.3539
MA0136.10.167861
MA0139.10.114954
MA0140.11.67276
MA0141.10.121639
MA0142.10.0460474
MA0143.10.229607
MA0144.10.641364
MA0145.10.0484584
MA0146.10.00080301
MA0147.10.0200315
MA0148.11.43569
MA0149.10.0382154
MA0062.20.00508764
MA0035.20.429575
MA0039.20.109932
MA0138.20.0283091
MA0002.20.278272
MA0137.20.0768047
MA0104.20.0280894
MA0047.20.624551
MA0112.20.213549
MA0065.20.276839
MA0150.10.160815
MA0151.10
MA0152.10.25836
MA0153.10.173628
MA0154.10.172391
MA0155.10.131706
MA0156.10.0353024
MA0157.10.151616
MA0158.10
MA0159.10.0866089
MA0160.10.213762
MA0161.10
MA0162.11.15292e-07
MA0163.10.00337436
MA0164.10.463933
MA0080.20.0019223
MA0018.20.0183959
MA0099.20.258964
MA0079.21.22174e-06
MA0102.20.494276
MA0258.10.434321
MA0259.10.0516452
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

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