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Coexpression cluster:C617: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.568865,MA0004.1;2.12862,MA0006.1;0.152601,MA0007.1;0.260673,MA0009.1;0.695988,MA0014.1;0.0988823,MA0017.1;0.181071,MA0019.1;1.04045,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.164086,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.792277,MA0042.1;1.34583,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;0.110534,MA0050.1;0.265714,MA0051.1;1.685,MA0052.1;0.623986,MA0055.1;1.24095,MA0056.1;0,MA0057.1;0.254521,MA0058.1;3.23373,MA0059.1;4.07839,MA0060.1;0.0773489,MA0061.1;0.224865,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.385025,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;0.329767,MA0072.1;0.666958,MA0073.1;0.385259,MA0074.1;0.358953,MA0076.1;0.609177,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.199203,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.491738,MA0089.1;0,MA0090.1;0.635809,MA0091.1;1.39427,MA0092.1;0.691297,MA0093.1;2.81524,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.1571,MA0103.1;1.41401,MA0105.1;0.430023,MA0106.1;0.399649,MA0107.1;0.708233,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.660878,MA0113.1;0.414278,MA0114.1;0.104181,MA0115.1;0.929032,MA0116.1;0.10959,MA0117.1;0.732,MA0119.1;3.11614,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.0564547,MA0140.1;0.327488,MA0141.1;0.197753,MA0142.1;0.514195,MA0143.1;1.06513,MA0144.1;0.0953756,MA0145.1;0.324645,MA0146.1;0.548423,MA0147.1;1.19725,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.0599644,MA0035.2;0.872194,MA0039.2;1.04569,MA0138.2;0.44894,MA0002.2;0.906125,MA0137.2;0.168782,MA0104.2;0.952142,MA0047.2;0.388882,MA0112.2;0.30305,MA0065.2;0.0634018,MA0150.1;0.218956,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;0.0196232,MA0155.1;0.283527,MA0156.1;0.170442,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.361202,MA0160.1;0.30953,MA0161.1;0,MA0162.1;0.03301,MA0163.1;0.475256,MA0164.1;0.425415,MA0080.2;0.46983,MA0018.2;0.400879,MA0099.2;0.333432,MA0079.2;0.711847,MA0102.2;1.22472,MA0258.1;0.624652,MA0259.1;0.374338,MA0442.1;0
}}
}}

Revision as of 19:19, 22 January 2013


Full id: C617_mucinous_gall_signet_bile_maxillary_keratoacanthoma_Alveolar



Phase1 CAGE Peaks

Hg19::chr10:88106150..88106156,+p@chr10:88106150..88106156
+
Hg19::chr11:70781237..70781270,-p@chr11:70781237..70781270
-
Hg19::chr13:99644885..99644901,+p@chr13:99644885..99644901
+
Hg19::chr14:102196739..102196744,+p1@LINC00239
Hg19::chr16:16011740..16011741,-p@chr16:16011740..16011741
-
Hg19::chr16:52028463..52028468,-p@chr16:52028463..52028468
-
Hg19::chr16:52028472..52028487,-p@chr16:52028472..52028487
-
Hg19::chr16:52028503..52028515,-p@chr16:52028503..52028515
-
Hg19::chr1:240996509..240996525,-p@chr1:240996509..240996525
-
Hg19::chr20:62321640..62321645,+p1@BC131817
Hg19::chr5:172722414..172722417,-p@chr5:172722414..172722417
-
Hg19::chr6:31080343..31080359,-p1@C6orf15
Hg19::chr7:55757275..55757282,-p1@FKBP9L
Hg19::chr7:73118172..73118185,-p3@STX1A


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:0050796regulation of insulin secretion0.0214651323421493
GO:0030073insulin secretion0.0214651323421493
GO:0046883regulation of hormone secretion0.0214651323421493
GO:0030072peptide hormone secretion0.0214651323421493
GO:0002790peptide secretion0.0214651323421493
GO:0005484SNAP receptor activity0.0274245201189629
GO:0046879hormone secretion0.0274245201189629
GO:0015833peptide transport0.0275212931074951
GO:0051046regulation of secretion0.0369868979872323
GO:0003001generation of a signal involved in cell-cell signaling0.0394816897354447
GO:0006836neurotransmitter transport0.0399850147348268



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
bile duct9.07e-186
digestive system duct9.07e-186
biliary system2.45e-129
biliary tree2.45e-129
biliary bud2.45e-129
female gonad5.28e-0913
Disease
Ontology termp-valuen
cystadenocarcinoma9.37e-991
mucinous cystadenocarcinoma9.37e-991


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)
MA0003.10.568865
MA0004.12.12862
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.0988823
MA0017.10.181071
MA0019.11.04045
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.792277
MA0042.11.34583
MA0043.10.69629
MA0046.10.685589
MA0048.10.110534
MA0050.10.265714
MA0051.11.685
MA0052.10.623986
MA0055.11.24095
MA0056.10
MA0057.10.254521
MA0058.13.23373
MA0059.14.07839
MA0060.10.0773489
MA0061.10.224865
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.385025
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.385259
MA0074.10.358953
MA0076.10.609177
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.491738
MA0089.10
MA0090.10.635809
MA0091.11.39427
MA0092.10.691297
MA0093.12.81524
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.11.41401
MA0105.10.430023
MA0106.10.399649
MA0107.10.708233
MA0108.20.540797
MA0109.10
MA0111.10.660878
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.13.11614
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.11.06513
MA0144.10.0953756
MA0145.10.324645
MA0146.10.548423
MA0147.11.19725
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.872194
MA0039.21.04569
MA0138.20.44894
MA0002.20.906125
MA0137.20.168782
MA0104.20.952142
MA0047.20.388882
MA0112.20.30305
MA0065.20.0634018
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0196232
MA0155.10.283527
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.03301
MA0163.10.475256
MA0164.10.425415
MA0080.20.46983
MA0018.20.400879
MA0099.20.333432
MA0079.20.711847
MA0102.21.22472
MA0258.10.624652
MA0259.10.374338
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#290844.278006666049440.01156838455163820.0422873023061334



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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