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Coexpression cluster:C1489: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.555913,0.553339,0.707204,0.223349,0.650887,1.01544,0.415981,0.889639,0.336106,0.236034,0.402028,0.436569,1.03374,0.576478,0.387783,0.483957,0.730467,1.10781,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.316592,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.323162,0.390088,0.154075,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,1.63739,0.272514,1.10535,0.0481066,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.90555
|tfbs_overrepresentation_jaspar=MA0003.1;0.026277,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.108006,MA0017.1;1.10421,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.05129,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;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.213007,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.671725,MA0063.1;0,MA0066.1;3.92151,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;2.33031,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00076337,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;0.0971959,MA0089.1;0,MA0090.1;1.22966,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.419295,MA0106.1;0.70837,MA0107.1;0.857383,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;1.12205,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;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.441872,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;0.200862,MA0138.2;0.765223,MA0002.2;1.3092,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;1.12726,MA0065.2;1.18263,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.875329,MA0160.1;1.46233,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.0270301,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.0318308,MA0102.2;1.58513,MA0258.1;1.43672,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:58, 22 January 2013


Full id: C1489_colon_Hepatocyte_liver_small_adenocarcinoma_hepatocellular_duodenum



Phase1 CAGE Peaks

Hg19::chr21:44859375..44859383,-p@chr21:44859375..44859383
-
Hg19::chr2:88425813..88425828,-p2@BX641099
Hg19::chr2:88425833..88425845,-p1@BX641099
Hg19::chr2:88427571..88427590,-p1@FABP1
Hg19::chr3:195943369..195943392,+p2@OSTalpha
Hg19::chr5:66307148..66307152,-p@chr5:66307148..66307152
-


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

No GOStat results

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 cell8.86e-2012
endopolyploid cell8.86e-2012
parenchymal cell8.86e-2012
polyploid cell8.86e-2012
hepatocyte8.86e-2012
endodermal cell9.33e-0858
intestinal epithelial cell3.13e-074
Uber Anatomy
Ontology termp-valuen
intestine1.58e-3417
gastrointestinal system3.54e-2825
digestive tract diverticulum3.98e-2223
liver1.50e-2119
digestive gland1.50e-2119
liver bud1.50e-2119
large intestine7.41e-2111
subdivision of digestive tract4.37e-20118
sac2.09e-1926
hepatic diverticulum1.87e-1822
liver primordium1.87e-1822
colon4.99e-189
digestive system2.67e-17145
digestive tract2.67e-17145
primitive gut2.67e-17145
epithelial sac4.24e-1625
epithelium of foregut-midgut junction4.24e-1625
anatomical boundary4.24e-1625
hepatobiliary system4.24e-1625
foregut-midgut junction4.24e-1625
septum transversum4.24e-1625
endoderm-derived structure2.79e-15160
endoderm2.79e-15160
presumptive endoderm2.79e-15160
gut epithelium3.35e-1554
endocrine gland5.82e-1435
exocrine gland9.38e-1331
exocrine system9.38e-1331
abdomen element1.00e-1254
abdominal segment element1.00e-1254
small intestine1.40e-124
lower digestive tract4.82e-125
abdominal segment of trunk2.98e-1160
abdomen2.98e-1160
endocrine system1.56e-1045
organ system subdivision1.33e-09223
gland1.77e-0959
endo-epithelium3.05e-0982
vermiform appendix9.72e-081
caecum9.72e-081
midgut9.72e-081
rectum2.84e-074
intestinal mucosa3.13e-074
wall of intestine3.13e-074
gastrointestinal system mucosa3.13e-074
gastrointestinal system epithelium3.13e-074
intestinal epithelium3.13e-074
trunk region element4.44e-07101
multi-tissue structure4.94e-07342


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.13.92151
MA0067.11.35893
MA0068.10.199491
MA0069.12.33031
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.11.12205
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
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.441872
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.21.3092
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.21.12726
MA0065.21.18263
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.11.46233
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.0318308
MA0102.21.58513
MA0258.11.43672
MA0259.10.336472
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
HEY1#2346253.366759202588090.004423827045203030.0209532912822657



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:C1489&oldid=2570000"