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Coexpression cluster:C1469: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,1.36287,0.267027,0.555913,0.553339,0.707204,1.18908,0.650887,0.391663,0.415981,2.06078,0.336106,1.23744,0.127969,0.436569,0.0880431,1.41165,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,1.31499,0.92701,0.302275,0.225641,0.35719,1.30732,3.4547,0.585658,0.329602,0.248856,0.936389,0.513952,0.0979105,0.390088,1.41477,1.18176,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,1.59978,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,1.41895,1.15727,1.82876,1.12235,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.406668,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,0.32338,0.234532,0.987239,0.776336,3.72085,0.330999,0.938327,0.981588,0.893363,1.90697,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.800507,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,3.17488,0.611524,0.799467,2.01411,0.510514,2.2813,0.8388,0.308967,1.07915,0.717973,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,3.39081
|tfbs_overrepresentation_jaspar=MA0003.1;8.45809,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;1.56589,MA0017.1;0.432438,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;1.45353,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;1.71708,MA0056.1;0,MA0057.1;1.41984,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;2.71441,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;1.53717,MA0074.1;1.58758,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;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.81721,MA0103.1;0.381434,MA0105.1;3.35204,MA0106.1;0.70837,MA0107.1;1.54633,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.865577,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;1.86787,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.347815,MA0146.1;0.232472,MA0147.1;0.87383,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;3.23723,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;1.87543,MA0104.2;1.35181,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.718489,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;1.57484,MA0160.1;0.600559,MA0161.1;0,MA0162.1;1.87239,MA0163.1;5.08954,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;2.58359,MA0079.2;4.35479,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1469_kidney_amniotic_liver_Hepatocyte_Placental_Amniotic_tongue



Phase1 CAGE Peaks

Hg19::chr1:204120903..204120917,-p6@ETNK2
Hg19::chr1:204120920..204120929,-p12@ETNK2
Hg19::chr1:204120931..204120942,-p10@ETNK2
Hg19::chr1:204120945..204120958,-p11@ETNK2
Hg19::chr1:47603109..47603120,+p1@CYP4A22
Hg19::chr2:135595876..135595891,+p3@ACMSD


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

p.valueFDRnGenesnPathwayName
6.31961929821581e-050.040003190157706131138Metabolic pathways (KEGG):01100



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:0046874quinolinate metabolic process0.00141292829388908
GO:0001760aminocarboxymuconate-semialdehyde decarboxylase activity0.00141292829388908
GO:0004305ethanolamine kinase activity0.00211926766548736
GO:0004103choline kinase activity0.00211926766548736
GO:0043648dicarboxylic acid metabolic process0.00903874877915148
GO:0016831carboxy-lyase activity0.0263319827971826
GO:0016830carbon-carbon lyase activity0.0330240233239064



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
extraembryonic cell9.00e-1219
placental epithelial cell9.73e-083
astrocyte of the cerebellum7.92e-073
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane4.54e-1414
membranous layer4.54e-1414
abdomen element4.12e-1054
abdominal segment element4.12e-1054
gland1.35e-0959
reproductive structure1.39e-0959
reproductive system1.39e-0959
endoderm-derived structure1.43e-09160
endoderm1.43e-09160
presumptive endoderm1.43e-09160
male organism6.54e-0922
male reproductive system6.54e-0922
extraembryonic structure9.65e-0924
male reproductive organ1.07e-0811
subdivision of digestive tract1.26e-08118
abdominal segment of trunk1.41e-0860
abdomen1.41e-0860
digestive system1.82e-08145
digestive tract1.82e-08145
primitive gut1.82e-08145
reproductive organ3.76e-0848
organ3.83e-08503
urinary system structure4.18e-0847
amnion4.59e-087
trunk region element4.82e-08101
renal system7.52e-0848
adult organism7.66e-08114
liver9.05e-0819
digestive gland9.05e-0819
liver bud9.05e-0819
chorion1.26e-077
exocrine gland1.63e-0731
exocrine system1.63e-0731
gut epithelium2.01e-0754
mixed endoderm/mesoderm-derived structure2.35e-0729
organ system subdivision4.89e-07223
somatic layer of lateral plate mesoderm5.59e-078
immaterial anatomical entity5.83e-07117
endocrine gland6.90e-0735
segmental subdivision of hindbrain8.03e-0712
hindbrain8.03e-0712
presumptive hindbrain8.03e-0712


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)
MA0003.18.45809
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.56589
MA0017.10.432438
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
MA0048.11.45353
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.11.41984
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.12.71441
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.11.53717
MA0074.11.58758
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.81721
MA0103.10.381434
MA0105.13.35204
MA0106.10.70837
MA0107.11.54633
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
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
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.232472
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.23.23723
MA0138.20.765223
MA0002.20.255126
MA0137.21.87543
MA0104.21.35181
MA0047.20.695777
MA0112.20.101413
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.11.57484
MA0160.10.600559
MA0161.10
MA0162.11.87239
MA0163.15.08954
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.22.58359
MA0079.24.35479
MA0102.21.58513
MA0258.10.289793
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
CEBPB#105145.314098417216540.003008047293917460.0159811502354993
NR3C1#290849.982015554115360.0002673219180401920.00286082936757861
ZBTB7A#5134144.901272871917260.004079628118843750.0194891721299022



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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