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Coexpression cluster:C3532: Difference between revisions

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{{Coexpression_clusters
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receptor activity!0.00405480984340045!6755$GO:0050796!regulation of insulin secretion!0.00405480984340045!6755$GO:0030073!insulin secretion!0.00405480984340045!6755$GO:0042593!glucose homeostasis!0.00405480984340045!6755$GO:0033500!carbohydrate homeostasis!0.00405480984340045!6755$GO:0030072!peptide hormone secretion!0.00405480984340045!6755$GO:0002790!peptide secretion!0.00405480984340045!6755$GO:0046883!regulation of hormone secretion!0.00405480984340045!6755$GO:0046879!hormone secretion!0.00644975600821592!6755$GO:0015833!peptide transport!0.00665842458495231!6755$GO:0008188!neuropeptide receptor activity!0.00697142745005691!6755$GO:0042923!neuropeptide binding!0.00697142745005691!6755$GO:0051046!regulation of secretion!0.00774846253475713!6755$GO:0003001!generation of a signal involved in cell-cell signaling!0.00853644177557989!6755$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0126339338278582!6755$GO:0019935!cyclic-nucleotide-mediated 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0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.0750181|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,0.680949,3.26509,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,1.86765,1.21459,0.534793,1.11965,1.46099,1.36391,0.596053,1.99037,0.567465,0.469078,0.598234,0.777097,2.04167,0.63803,0.151453,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,1.82176,2.29164,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,1.96295|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,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;1.67416,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;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.407479,MA0074.1;0.935474,MA0076.1;0.734647,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;0.257905,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;0.628063,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;3.4624,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,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;0.432958,MA0138.2;1.04628,MA0002.2;3.08747,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;2.47657,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;1.2663,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=C3532_tubular_signet_smallcell_argyrophil_prostate_tonsil_somatostatinoma
|id=C3532
}}

Latest revision as of 12:28, 17 September 2013


Full id: C3532_tubular_signet_smallcell_argyrophil_prostate_tonsil_somatostatinoma



Phase1 CAGE Peaks

Hg19::chr16:1117848..1117886,-p@chr16:1117848..1117886
-
Hg19::chr16:1128614..1128627,-p1@LOC146336
Hg19::chr16:1128813..1128840,+p1@SSTR5


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:0004994somatostatin receptor activity0.00405480984340045
GO:0050796regulation of insulin secretion0.00405480984340045
GO:0030073insulin secretion0.00405480984340045
GO:0042593glucose homeostasis0.00405480984340045
GO:0033500carbohydrate homeostasis0.00405480984340045
GO:0030072peptide hormone secretion0.00405480984340045
GO:0002790peptide secretion0.00405480984340045
GO:0046883regulation of hormone secretion0.00405480984340045
GO:0046879hormone secretion0.00644975600821592
GO:0015833peptide transport0.00665842458495231
GO:0008188neuropeptide receptor activity0.00697142745005691
GO:0042923neuropeptide binding0.00697142745005691
GO:0051046regulation of secretion0.00774846253475713
GO:0003001generation of a signal involved in cell-cell signaling0.00853644177557989
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0126339338278582
GO:0019935cyclic-nucleotide-mediated signaling0.0126339338278582
GO:0030594neurotransmitter receptor activity0.0126339338278582
GO:0042165neurotransmitter binding0.0126339338278582
GO:0001653peptide receptor activity0.0126339338278582
GO:0008528peptide receptor activity, G-protein coupled0.0126339338278582
GO:0042277peptide binding0.0169102846601963
GO:0008285negative regulation of cell proliferation0.017460903631868
GO:0019932second-messenger-mediated signaling0.0198936208335253
GO:0048878chemical homeostasis0.0214833784685427
GO:0046903secretion0.0262239491345814
GO:0042127regulation of cell proliferation0.0303517929798396
GO:0042592homeostatic process0.0303517929798396
GO:0007267cell-cell signaling0.0390237338312223
GO:0008283cell proliferation0.043859649122807



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
throat7.26e-082
Disease
Ontology termp-valuen
carcinoma1.18e-12106
cell type cancer9.63e-11143
cancer1.44e-08235
disease of cellular proliferation3.13e-08239
signet ring cell adenocarcinoma4.31e-082
adenocarcinoma6.77e-0825
cervical cancer4.29e-075


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)
MA0003.10.401049
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
MA0055.11.67416
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
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
MA0116.13.4624
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
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
MA0039.20.432958
MA0138.21.04628
MA0002.23.08747
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.12.47657
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.2663
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BHLHE40#8553229.91454236465160.001467483527106140.00939511506696737
BRCA1#672213.45615376214920.007119807716084560.0296190240215158
FOSL2#2355211.28680040304110.0100534586973120.0376671990273924
FOXA2#3170216.42030916844350.004810682352105480.0225848626347004
GATA3#2625218.15767757147070.003944546819279620.0189452529436074
RXRA#6256213.38307809275550.007196434429465730.029823753635926
SMC3#9126210.02995522995520.0126656379767470.0457284393353435



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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