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Coexpression cluster:C242: Difference between revisions

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{{Coexpression_clusters
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macromolecule catabolic process!0.0426517274003166!5657$GO:0000184!mRNA catabolic process, nonsense-mediated decay!0.0426517274003166!255967$GO:0044243!multicellular organismal catabolic process!0.0426517274003166!5657$GO:0032963!collagen metabolic process!0.0426517274003166!5657$GO:0044236!multicellular organismal metabolic process!0.0426517274003166!5657$GO:0005694!chromosome!0.0426517274003166!56033;9425$GO:0004468!lysine N-acetyltransferase activity!0.0426517274003166!9425$GO:0004402!histone acetyltransferase activity!0.0426517274003166!9425$GO:0030111!regulation of Wnt receptor signaling pathway!0.0426517274003166!56033$GO:0002274!myeloid leukocyte activation!0.0426517274003166!7462$GO:0050851!antigen receptor-mediated signaling pathway!0.0426517274003166!7462$GO:0006402!mRNA catabolic process!0.0426517274003166!255967$GO:0002429!immune response-activating cell surface receptor signaling pathway!0.0426517274003166!7462$GO:0002768!immune response-regulating cell surface receptor 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.286487,0.154784,0.293514,0.858172,0.0996003,0.0252006,1.5393,0.0531207,0.0687874,0.660526,0.105515,0.0672025,0.189708,0.199364,0.160386,0.333078,0.330306,0.0019644,1.2734,0.00185694,0.0270909,0.617155,0.105591,1.30111,0.0682575,0.138439,1.21711,0.0605156,0.00906634,0.177275,0.213927,0.523341,0.459489,0.0742228,0.0504245,1.1071,0.206493,0.3112,0.0439253,0.701119,0.139972,0.403938,0.139139,0.184367,0.0475061,0.708475,0.125651,0.0531551,0.35199,0.378202,0.691489,0.914343,0.548044,0.162852,0.151256,0.00422723,0.309732,0.0119317,0.0509513,0.312277,0.117199,0.90676,0.483927,0.959482,0.125106,0.434885,0.145691,0.272815,0.000165807,0.00524792,0.679009,0.600832,0.782327,0.453124,0.254109,0.17005,0.528379,0.0207649,0.588798,0.15151,0.195616,0.292689,1.11292,1.12455,0.166773,0.192184,0.861635,0.103341,0.0199953,0.416597,0.371028,0.144474,0.0166347,0.633387,0.19049,0.362069,0.022591,0.414117,0.0987639,0.0012793,0.0168582,0.349067,0.541278,0.303681,1.491,0.268322,1.68989,0.505391,0.117574,1.50202,0.17297,0.335239,0.0279198,0.254581,0.648062,0.346113,0.204131,0.463748,0.343562,0.620149,0.48437,0.428994,1.21559,0.830963,0.399057,0.172002,0.564198,1.14591,0.90252,1.61282,1.06153,0.577983,0.0565584,0.0364321,1.20586e-05,1.30814,0.326658,1.54682,0.574568,0.268919,0.129208,0.144818,0.114703,0.398092,0.242284,0.904924,0.0416172,0.111757,0.195535,0.0473842,0.699174,0.083549|tfbs_overrepresentation_jaspar=MA0003.1;0.00035258,MA0004.1;0.0950574,MA0006.1;0.0636978,MA0007.1;0.21013,MA0009.1;0.226788,MA0014.1;0.00436367,MA0017.1;0.36614,MA0019.1;0.48606,MA0024.1;0.161864,MA0025.1;0.858925,MA0027.1;1.69083,MA0028.1;0.0757086,MA0029.1;0.173144,MA0030.1;0.166414,MA0031.1;0.13071,MA0038.1;0.0473031,MA0040.1;0.176624,MA0041.1;0.491879,MA0042.1;0.0861492,MA0043.1;0.643845,MA0046.1;1.17481,MA0048.1;0.0981386,MA0050.1;0.086722,MA0051.1;0.17489,MA0052.1;1.01455,MA0055.1;0.772405,MA0056.1;0,MA0057.1;0.0861015,MA0058.1;0.248826,MA0059.1;0.24649,MA0060.1;0.071183,MA0061.1;0.00128149,MA0063.1;0,MA0066.1;0.179263,MA0067.1;0.466752,MA0068.1;0.000400878,MA0069.1;0.620599,MA0070.1;0.209894,MA0071.1;0.0362647,MA0072.1;0.207017,MA0073.1;0.000937115,MA0074.1;0.393105,MA0076.1;0.27844,MA0077.1;0.584975,MA0078.1;0.0816416,MA0081.1;0.430446,MA0083.1;0.231773,MA0084.1;0.628386,MA0087.1;0.592935,MA0088.1;0.0166025,MA0089.1;0,MA0090.1;0.0563452,MA0091.1;1.07875,MA0092.1;0.368747,MA0093.1;0.0658755,MA0095.1;0,MA0098.1;0,MA0100.1;0.0516781,MA0101.1;0.0218059,MA0103.1;0.250578,MA0105.1;0.000768518,MA0106.1;0.219819,MA0107.1;0.0263037,MA0108.2;1.30889,MA0109.1;0,MA0111.1;0.168097,MA0113.1;0.237178,MA0114.1;0.373995,MA0115.1;0.404335,MA0116.1;0.145567,MA0117.1;0.252146,MA0119.1;0.386627,MA0122.1;0.743919,MA0124.1;0.371502,MA0125.1;0.829108,MA0130.1;0,MA0131.1;0.0893561,MA0132.1;0,MA0133.1;0,MA0135.1;0.247187,MA0136.1;0.729974,MA0139.1;0.331953,MA0140.1;0.599233,MA0141.1;0.243356,MA0142.1;0.114579,MA0143.1;0.51078,MA0144.1;0.0516892,MA0145.1;0.0252698,MA0146.1;0.0287776,MA0147.1;0.15144,MA0148.1;0.112894,MA0149.1;0.0331094,MA0062.2;0.0831258,MA0035.2;0.329382,MA0039.2;0.000480551,MA0138.2;0.0821519,MA0002.2;0.634583,MA0137.2;0.0808931,MA0104.2;0.354713,MA0047.2;0.056737,MA0112.2;0.220422,MA0065.2;0.612136,MA0150.1;0.145397,MA0151.1;0,MA0152.1;0.616446,MA0153.1;0.29535,MA0154.1;1.08015,MA0155.1;0.463488,MA0156.1;0.526995,MA0157.1;0.332779,MA0158.1;0,MA0159.1;0.0295222,MA0160.1;0.124604,MA0161.1;0,MA0162.1;1.15568e-05,MA0163.1;0.00299633,MA0164.1;0.912151,MA0080.2;1.97139,MA0018.2;0.22126,MA0099.2;0.147733,MA0079.2;3.79317e-07,MA0102.2;0.661673,MA0258.1;0.444615,MA0259.1;0.0827141,MA0442.1;0}}
|full_id=C242_acute_Chondrocyte_myelodysplastic_granulocyte_biphenotypic_Fibroblast_stomach
|id=C242
}}

Latest revision as of 11:04, 17 September 2013


Full id: C242_acute_Chondrocyte_myelodysplastic_granulocyte_biphenotypic_Fibroblast_stomach



Phase1 CAGE Peaks

Hg19::chr10:11894144..11894162,+p@chr10:11894144..11894162
+
Hg19::chr10:134257886..134257894,+p5@C10orf91
Hg19::chr10:91731546..91731549,+p@chr10:91731546..91731549
+
Hg19::chr11:86133182..86133185,+p@chr11:86133182..86133185
+
Hg19::chr12:117102463..117102470,+p@chr12:117102463..117102470
+
Hg19::chr13:28620069..28620072,-p@chr13:28620069..28620072
-
Hg19::chr13:28813645..28813656,+p25@PAN3
Hg19::chr13:51484041..51484052,+p8@RNASEH2B
Hg19::chr15:99819658..99819672,+p@chr15:99819658..99819672
+
Hg19::chr16:61278581..61278587,-p@chr16:61278581..61278587
-
Hg19::chr16:85887504..85887515,+p@chr16:85887504..85887515
+
Hg19::chr16:85887549..85887557,+p@chr16:85887549..85887557
+
Hg19::chr17:37865499..37865505,+p@chr17:37865499..37865505
+
Hg19::chr17:37865552..37865557,+p@chr17:37865552..37865557
+
Hg19::chr17:67044013..67044015,+p@chr17:67044013..67044015
+
Hg19::chr17:80626054..80626077,-p@chr17:80626054..80626077
-
Hg19::chr18:74846147..74846167,-p@chr18:74846147..74846167
-
Hg19::chr19:843314..843331,+p4@PRTN3
Hg19::chr1:108093162..108093168,-p@chr1:108093162..108093168
-
Hg19::chr1:72566627..72566642,-p10@NEGR1
Hg19::chr1:91123303..91123309,+p1@ENST00000362796
Hg19::chr20:9491247..9491276,+p@chr20:9491247..9491276
+
Hg19::chr20:9491287..9491294,+p@chr20:9491287..9491294
+
Hg19::chr2:22534257..22534264,+p@chr2:22534257..22534264
+
Hg19::chr2:22534265..22534281,+p@chr2:22534265..22534281
+
Hg19::chr2:22534311..22534316,+p@chr2:22534311..22534316
+
Hg19::chr2:22534322..22534329,+p@chr2:22534322..22534329
+
Hg19::chr3:128578615..128578626,-p@chr3:128578615..128578626
-
Hg19::chr3:18020939..18020953,+p@chr3:18020939..18020953
+
Hg19::chr3:18020966..18020978,+p@chr3:18020966..18020978
+
Hg19::chr3:18020982..18021001,+p@chr3:18020982..18021001
+
Hg19::chr3:18021007..18021028,+p@chr3:18021007..18021028
+
Hg19::chr3:18110143..18110146,+p@chr3:18110143..18110146
+
Hg19::chr3:18178615..18178618,+p@chr3:18178615..18178618
+
Hg19::chr3:18344317..18344322,+p@chr3:18344317..18344322
+
Hg19::chr4:47432804..47432808,-p@chr4:47432804..47432808
-
Hg19::chr4:47443248..47443256,-p@chr4:47443248..47443256
-
Hg19::chr4:47445162..47445167,-p@chr4:47445162..47445167
-
Hg19::chr4:47445183..47445188,-p@chr4:47445183..47445188
-
Hg19::chr4:47445237..47445246,-p@chr4:47445237..47445246
-
Hg19::chr5:120617659..120617660,+p@chr5:120617659..120617660
+
Hg19::chr5:164566956..164566970,+p@chr5:164566956..164566970
+
Hg19::chr6:14657070..14657092,-p@chr6:14657070..14657092
-
Hg19::chr6:4890245..4890276,+p18@CDYL
Hg19::chr6:5034746..5034769,-p@chr6:5034746..5034769
-
Hg19::chr7:1548199..1548208,-p@chr7:1548199..1548208
-
Hg19::chr7:1548370..1548414,-p@chr7:1548370..1548414
-
Hg19::chr7:43150627..43150647,+p@chr7:43150627..43150647
+
Hg19::chr7:73634762..73634776,+p5@LAT2
Hg19::chr8:121737322..121737328,+p@chr8:121737322..121737328
+
Hg19::chr8:143591583..143591596,+p@chr8:143591583..143591596
+
Hg19::chr8:144488686..144488699,+p@chr8:144488686..144488699
+
Hg19::chr8:144488798..144488834,+p@chr8:144488798..144488834
+
Hg19::chr9:139927093..139927113,+p7@C9orf139
Hg19::chr9:214096..214121,+p@chr9:214096..214121
+
Hg19::chr9:96717629..96717644,-p1@BARX1


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:0043303mast cell degranulation0.0426517274003166
GO:0002448mast cell mediated immunity0.0426517274003166
GO:0045576mast cell activation0.0426517274003166
GO:0043299leukocyte degranulation0.0426517274003166
GO:0002444myeloid leukocyte mediated immunity0.0426517274003166
GO:0050853B cell receptor signaling pathway0.0426517274003166
GO:0043285biopolymer catabolic process0.0426517274003166
GO:0042169SH2 domain binding0.0426517274003166
GO:0030178negative regulation of Wnt receptor signaling pathway0.0426517274003166
GO:0030574collagen catabolic process0.0426517274003166
GO:0044259multicellular organismal macromolecule metabolic process0.0426517274003166
GO:0044268multicellular organismal protein metabolic process0.0426517274003166
GO:0044256protein digestion0.0426517274003166
GO:0044254multicellular organismal protein catabolic process0.0426517274003166
GO:0044266multicellular organismal macromolecule catabolic process0.0426517274003166
GO:0000184mRNA catabolic process, nonsense-mediated decay0.0426517274003166
GO:0044243multicellular organismal catabolic process0.0426517274003166
GO:0032963collagen metabolic process0.0426517274003166
GO:0044236multicellular organismal metabolic process0.0426517274003166
GO:0005694chromosome0.0426517274003166
GO:0004468lysine N-acetyltransferase activity0.0426517274003166
GO:0004402histone acetyltransferase activity0.0426517274003166
GO:0030111regulation of Wnt receptor signaling pathway0.0426517274003166
GO:0002274myeloid leukocyte activation0.0426517274003166
GO:0050851antigen receptor-mediated signaling pathway0.0426517274003166
GO:0006402mRNA catabolic process0.0426517274003166
GO:0002429immune response-activating cell surface receptor signaling pathway0.0426517274003166
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0426517274003166
GO:0002757immune response-activating signal transduction0.0426517274003166
GO:0009057macromolecule catabolic process0.0426517274003166
GO:0002764immune response-regulating signal transduction0.0426517274003166
GO:0030855epithelial cell differentiation0.0449074914160441
GO:0019722calcium-mediated signaling0.0449074914160441



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><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia7.41e-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)
MA0003.10.00035258
MA0004.10.0950574
MA0006.10.0636978
MA0007.10.21013
MA0009.10.226788
MA0014.10.00436367
MA0017.10.36614
MA0019.10.48606
MA0024.10.161864
MA0025.10.858925
MA0027.11.69083
MA0028.10.0757086
MA0029.10.173144
MA0030.10.166414
MA0031.10.13071
MA0038.10.0473031
MA0040.10.176624
MA0041.10.491879
MA0042.10.0861492
MA0043.10.643845
MA0046.11.17481
MA0048.10.0981386
MA0050.10.086722
MA0051.10.17489
MA0052.11.01455
MA0055.10.772405
MA0056.10
MA0057.10.0861015
MA0058.10.248826
MA0059.10.24649
MA0060.10.071183
MA0061.10.00128149
MA0063.10
MA0066.10.179263
MA0067.10.466752
MA0068.10.000400878
MA0069.10.620599
MA0070.10.209894
MA0071.10.0362647
MA0072.10.207017
MA0073.10.000937115
MA0074.10.393105
MA0076.10.27844
MA0077.10.584975
MA0078.10.0816416
MA0081.10.430446
MA0083.10.231773
MA0084.10.628386
MA0087.10.592935
MA0088.10.0166025
MA0089.10
MA0090.10.0563452
MA0091.11.07875
MA0092.10.368747
MA0093.10.0658755
MA0095.10
MA0098.10
MA0100.10.0516781
MA0101.10.0218059
MA0103.10.250578
MA0105.10.000768518
MA0106.10.219819
MA0107.10.0263037
MA0108.21.30889
MA0109.10
MA0111.10.168097
MA0113.10.237178
MA0114.10.373995
MA0115.10.404335
MA0116.10.145567
MA0117.10.252146
MA0119.10.386627
MA0122.10.743919
MA0124.10.371502
MA0125.10.829108
MA0130.10
MA0131.10.0893561
MA0132.10
MA0133.10
MA0135.10.247187
MA0136.10.729974
MA0139.10.331953
MA0140.10.599233
MA0141.10.243356
MA0142.10.114579
MA0143.10.51078
MA0144.10.0516892
MA0145.10.0252698
MA0146.10.0287776
MA0147.10.15144
MA0148.10.112894
MA0149.10.0331094
MA0062.20.0831258
MA0035.20.329382
MA0039.20.000480551
MA0138.20.0821519
MA0002.20.634583
MA0137.20.0808931
MA0104.20.354713
MA0047.20.056737
MA0112.20.220422
MA0065.20.612136
MA0150.10.145397
MA0151.10
MA0152.10.616446
MA0153.10.29535
MA0154.11.08015
MA0155.10.463488
MA0156.10.526995
MA0157.10.332779
MA0158.10
MA0159.10.0295222
MA0160.10.124604
MA0161.10
MA0162.11.15568e-05
MA0163.10.00299633
MA0164.10.912151
MA0080.21.97139
MA0018.20.22126
MA0099.20.147733
MA0079.23.79317e-07
MA0102.20.661673
MA0258.10.444615
MA0259.10.0827141
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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