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Coexpression cluster:C1363: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;1.37419,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,MA0017.1;1.935,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;2.33832,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.450439,MA0058.1;1.16137,MA0059.1;1.15845,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.347876,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.660742,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;1.02138,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.993014,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;1.52717,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;1.15452,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.811435,MA0145.1;0.347815,MA0146.1;0.093337,MA0147.1;0.87383,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.569061,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.735746,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;2.35074,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;0.65596,MA0156.1;1.07131,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.875329,MA0160.1;1.46233,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.113377,MA0164.1;1.74929,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.166826,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:53, 22 January 2013


Full id: C1363_pancreas_small_gall_temporal_duodenum_colon_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr12:56624532..56624554,+p2@SLC39A5
Hg19::chr16:3704849..3704860,+p4@DNASE1
Hg19::chr17:202392..202413,+p1@AK125265
Hg19::chr21:37091670..37091681,+p@chr21:37091670..37091681
+
Hg19::chr22:37975952..37975968,-p2@LGALS2
Hg19::chr2:79384252..79384270,-p@chr2:79384252..79384270
-


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:0004530deoxyribonuclease I activity0.0116566584245849



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
metabolising cell1.12e-2612
endopolyploid cell1.12e-2612
parenchymal cell1.12e-2612
polyploid cell1.12e-2612
hepatocyte1.12e-2612
endodermal cell6.07e-0958
Uber Anatomy
Ontology termp-valuen
intestine1.02e-3417
gastrointestinal system1.44e-3225
liver1.12e-2519
digestive gland1.12e-2519
liver bud1.12e-2519
digestive tract diverticulum2.76e-2523
large intestine3.34e-2311
epithelium of foregut-midgut junction4.37e-2325
anatomical boundary4.37e-2325
hepatobiliary system4.37e-2325
foregut-midgut junction4.37e-2325
septum transversum4.37e-2325
sac3.98e-2226
hepatic diverticulum6.25e-2222
liver primordium6.25e-2222
subdivision of digestive tract1.36e-20118
epithelial sac4.40e-1925
abdomen element1.34e-1854
abdominal segment element1.34e-1854
digestive system2.19e-17145
digestive tract2.19e-17145
primitive gut2.19e-17145
lower digestive tract2.44e-175
abdominal segment of trunk2.02e-1660
abdomen2.02e-1660
gut epithelium3.78e-1654
endoderm-derived structure2.92e-15160
endoderm2.92e-15160
presumptive endoderm2.92e-15160
exocrine gland4.85e-1531
exocrine system4.85e-1531
colon7.17e-159
endocrine gland4.08e-1335
rectum8.11e-134
endocrine system4.72e-1245
small intestine8.22e-114
trunk region element6.73e-10101
endo-epithelium1.19e-0982
organ system subdivision2.51e-09223
gland1.16e-0859
mesenchyme8.87e-08160
entire embryonic mesenchyme8.87e-08160
subdivision of trunk2.30e-07112
multi-tissue structure4.70e-07342
immaterial anatomical entity7.21e-07117
hindgut7.26e-0719


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)
MA0003.10.176622
MA0004.11.37419
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.11.935
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.12.33832
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.347876
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.10.347815
MA0146.10.093337
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.101413
MA0065.22.35074
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.65596
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.11.46233
MA0161.10
MA0162.10.0383129
MA0163.10.113377
MA0164.11.74929
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.166826
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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
ESRRA#2101180.6400523560210.01233705312615740.0447012729476392
HNF4G#3174419.16894835096452.07234608447467e-050.000458157816927286



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1363&oldid=2569874"