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Coexpression cluster:C3094: Difference between revisions

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{{Coexpression_clusters
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regulation of cGMP metabolic process!0.000392480081635857!79849$GO:0030823!regulation of cGMP metabolic process!0.000392480081635857!79849$GO:0035003!subapical complex!0.000392480081635857!79849$GO:0030826!regulation of cGMP biosynthetic process!0.000392480081635857!79849$GO:0030827!negative regulation of cGMP biosynthetic process!0.000392480081635857!79849$GO:0030251!guanylate cyclase inhibitor activity!0.000392480081635857!79849$GO:0019934!cGMP-mediated signaling!0.00067282299709004!79849$GO:0030803!negative regulation of cyclic nucleotide biosynthetic process!0.000706464146944542!79849$GO:0030800!negative regulation of cyclic nucleotide metabolic process!0.000706464146944542!79849$GO:0030809!negative regulation of nucleotide biosynthetic process!0.000706464146944542!79849$GO:0007168!receptor guanylyl cyclase signaling pathway!0.00100923449563506!79849$GO:0030802!regulation of cyclic nucleotide biosynthetic process!0.00100923449563506!79849$GO:0045980!negative regulation of nucleotide metabolic process!0.00100923449563506!79849$GO:0030808!regulation of nucleotide biosynthetic process!0.00100923449563506!79849$GO:0030799!regulation of cyclic nucleotide metabolic process!0.00103026021429412!79849$GO:0030249!guanylate cyclase regulator activity!0.00103026021429412!79849$GO:0006140!regulation of nucleotide metabolic process!0.00112624719078115!79849$GO:0008200!ion channel inhibitor activity!0.00112624719078115!79849$GO:0016248!channel inhibitor activity!0.00112624719078115!79849$GO:0046068!cGMP metabolic process!0.00112624719078115!79849$GO:0006182!cGMP biosynthetic process!0.00112624719078115!79849$GO:0006833!water transport!0.00112624719078115!79849$GO:0042044!fluid transport!0.00112624719078115!79849$GO:0009636!response to toxin!0.00235488048981514!79849$GO:0016247!channel regulator activity!0.0033910279053338!79849$GO:0009190!cyclic nucleotide biosynthetic process!0.00362289306125406!79849$GO:0009187!cyclic nucleotide metabolic process!0.00428924660644901!79849$GO:0009890!negative regulation of biosynthetic process!0.00428924660644901!79849$GO:0008022!protein C-terminus binding!0.00600900538780416!79849$GO:0045177!apical part of cell!0.00675065740413673!79849$GO:0043296!apical junction complex!0.00772695160720593!79849$GO:0016327!apicolateral plasma membrane!0.00772695160720593!79849$GO:0019935!cyclic-nucleotide-mediated signaling!0.00870592181083174!79849$GO:0005911!intercellular junction!0.0119821860217065!79849$GO:0009889!regulation of biosynthetic process!0.0146002590368539!79849$GO:0009165!nucleotide biosynthetic process!0.0166804034695239!79849$GO:0019932!second-messenger-mediated signaling!0.0170569721964989!79849$GO:0007167!enzyme linked receptor protein signaling pathway!0.0185911617616985!79849$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0192617147756674!79849$GO:0009117!nucleotide metabolic process!0.0200164841634287!79849$GO:0055086!nucleobase, nucleoside and nucleotide metabolic process!0.0210790521893209!79849$GO:0031324!negative regulation of cellular metabolic process!0.0213621301576088!79849$GO:0004857!enzyme inhibitor activity!0.02196062968409!79849$GO:0030054!cell junction!0.0228161754124311!79849$GO:0009892!negative regulation of metabolic process!0.0228161754124311!79849$GO:0005829!cytosol!0.0290776547438044!79849$GO:0042221!response to chemical stimulus!0.0295111618830025!79849$GO:0005624!membrane fraction!0.0335079869696613!79849$GO:0000267!cell 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3026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,1.40888,2.00385,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,2.72118,0.534793,0.439574,3.63468,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,1.73097,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.904546,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;2.0778,MA0072.1;1.29561,MA0073.1;1.36698,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;1.52002,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;1.12079,MA0140.1;2.07172,MA0141.1;1.6959,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;2.88736,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.941469,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3094_rectum_small_colon_Eosinophils_temporal_appendix_CD4
|id=C3094
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3094_rectum_small_colon_Eosinophils_temporal_appendix_CD4



Phase1 CAGE Peaks

Hg19::chr11:119056158..119056172,+p2@PDZD3
Hg19::chr1:2488426..2488475,-p1@LOC100133445
p1@LOC115110
Hg19::chr1:2488477..2488501,-p1@ENST00000452793


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:0030824negative regulation of cGMP metabolic process0.000392480081635857
GO:0030823regulation of cGMP metabolic process0.000392480081635857
GO:0035003subapical complex0.000392480081635857
GO:0030826regulation of cGMP biosynthetic process0.000392480081635857
GO:0030827negative regulation of cGMP biosynthetic process0.000392480081635857
GO:0030251guanylate cyclase inhibitor activity0.000392480081635857
GO:0019934cGMP-mediated signaling0.00067282299709004
GO:0030803negative regulation of cyclic nucleotide biosynthetic process0.000706464146944542
GO:0030800negative regulation of cyclic nucleotide metabolic process0.000706464146944542
GO:0030809negative regulation of nucleotide biosynthetic process0.000706464146944542
GO:0007168receptor guanylyl cyclase signaling pathway0.00100923449563506
GO:0030802regulation of cyclic nucleotide biosynthetic process0.00100923449563506
GO:0045980negative regulation of nucleotide metabolic process0.00100923449563506
GO:0030808regulation of nucleotide biosynthetic process0.00100923449563506
GO:0030799regulation of cyclic nucleotide metabolic process0.00103026021429412
GO:0030249guanylate cyclase regulator activity0.00103026021429412
GO:0006140regulation of nucleotide metabolic process0.00112624719078115
GO:0008200ion channel inhibitor activity0.00112624719078115
GO:0016248channel inhibitor activity0.00112624719078115
GO:0046068cGMP metabolic process0.00112624719078115
GO:0006182cGMP biosynthetic process0.00112624719078115
GO:0006833water transport0.00112624719078115
GO:0042044fluid transport0.00112624719078115
GO:0009636response to toxin0.00235488048981514
GO:0016247channel regulator activity0.0033910279053338
GO:0009190cyclic nucleotide biosynthetic process0.00362289306125406
GO:0009187cyclic nucleotide metabolic process0.00428924660644901
GO:0009890negative regulation of biosynthetic process0.00428924660644901
GO:0008022protein C-terminus binding0.00600900538780416
GO:0045177apical part of cell0.00675065740413673
GO:0043296apical junction complex0.00772695160720593
GO:0016327apicolateral plasma membrane0.00772695160720593
GO:0019935cyclic-nucleotide-mediated signaling0.00870592181083174
GO:0005911intercellular junction0.0119821860217065
GO:0009889regulation of biosynthetic process0.0146002590368539
GO:0009165nucleotide biosynthetic process0.0166804034695239
GO:0019932second-messenger-mediated signaling0.0170569721964989
GO:0007167enzyme linked receptor protein signaling pathway0.0185911617616985
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0192617147756674
GO:0009117nucleotide metabolic process0.0200164841634287
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0210790521893209
GO:0031324negative regulation of cellular metabolic process0.0213621301576088
GO:0004857enzyme inhibitor activity0.02196062968409
GO:0030054cell junction0.0228161754124311
GO:0009892negative regulation of metabolic process0.0228161754124311
GO:0005829cytosol0.0290776547438044
GO:0042221response to chemical stimulus0.0295111618830025
GO:0005624membrane fraction0.0335079869696613
GO:0000267cell fraction0.0433490245268012



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
hematopoietic lineage restricted progenitor cell3.48e-24120
leukocyte4.17e-24136
nongranular leukocyte6.33e-20115
hematopoietic oligopotent progenitor cell1.78e-18161
hematopoietic multipotent progenitor cell1.78e-18161
hematopoietic stem cell5.70e-18168
angioblastic mesenchymal cell5.70e-18168
nucleate cell5.89e-1855
lymphoid lineage restricted progenitor cell1.53e-1752
hematopoietic cell1.62e-17177
lymphocyte5.83e-1753
common lymphoid progenitor5.83e-1753
T cell2.02e-1025
pro-T cell2.02e-1025
mature alpha-beta T cell2.84e-0918
alpha-beta T cell2.84e-0918
immature T cell2.84e-0918
mature T cell2.84e-0918
immature alpha-beta T cell2.84e-0918
lymphocyte of B lineage3.22e-0824
pro-B cell3.22e-0824
myeloid leukocyte8.67e-0872
granulocyte monocyte progenitor cell1.71e-0767
myeloid lineage restricted progenitor cell1.84e-0766
CD8-positive, alpha-beta T cell9.58e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.16e-1498
blood island1.16e-1498
hemolymphoid system1.55e-12108
gastrointestinal system2.03e-0925
blood9.85e-0915
haemolymphatic fluid9.85e-0915
organism substance9.85e-0915
immune system1.83e-0793
subdivision of digestive tract2.28e-07118


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.12.0778
MA0072.11.29561
MA0073.11.36698
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.12.07172
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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

This analysis result is provided for C0 - C305 clusters.

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