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Coexpression cluster:C1362: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.515118,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,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;2.02362,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;0.0586456,MA0056.1;0,MA0057.1;2.74001,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;2.43863,MA0069.1;1.02175,MA0070.1;2.30704,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;53.0108,MA0074.1;3.89731,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,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;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;1.25994,MA0113.1;0.725375,MA0114.1;0.314898,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;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,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;0.26661,MA0047.2;0.695777,MA0112.2;2.25875,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;1.52275,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;4.31015,MA0156.1;0.417278,MA0157.1;1.89858,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;3.59546,MA0163.1;0.0270301,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;7.49373,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:53, 22 January 2013


Full id: C1362_Preadipocyte_Adipocyte_Fibroblast_Mesenchymal_mesenchymal_Myoblast_Smooth



Phase1 CAGE Peaks

Hg19::chr12:54402694..54402705,+p5@HOXC8
Hg19::chr12:54402729..54402743,+p3@HOXC8
Hg19::chr12:54402745..54402788,+p1@HOXC8
Hg19::chr12:54402790..54402805,+p2@HOXC8
Hg19::chr12:54410639..54410659,+p2@HOXC4
p2@HOXC5
p2@HOXC6
Hg19::chr12:54410664..54410684,+p1@HOXC4
p1@HOXC5
p1@HOXC6


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:0043565sequence-specific DNA binding0.0289572869453141
GO:0003700transcription factor activity0.0355826006899583
GO:0007275multicellular organismal development0.0355826006899583
GO:0032502developmental process0.0355826006899583
GO:0006355regulation of transcription, DNA-dependent0.0355826006899583
GO:0006351transcription, DNA-dependent0.0355826006899583
GO:0032774RNA biosynthetic process0.0355826006899583
GO:0003677DNA binding0.0355826006899583
GO:0045449regulation of transcription0.0355826006899583
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0355826006899583
GO:0030182neuron differentiation0.0355826006899583
GO:0006350transcription0.0355826006899583
GO:0032501multicellular organismal process0.0355826006899583
GO:0010468regulation of gene expression0.0355826006899583
GO:0031323regulation of cellular metabolic process0.0355826006899583
GO:0048699generation of neurons0.0355826006899583
GO:0019222regulation of metabolic process0.0355826006899583
GO:0016070RNA metabolic process0.0355826006899583
GO:0022008neurogenesis0.0355826006899583



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
fat cell6.85e-1215
skin fibroblast1.53e-1123
preadipocyte6.06e-1112
fibroblast9.20e-1176
mesenchymal stem cell of adipose1.99e-078
non-terminally differentiated cell3.08e-07106
Uber Anatomy
Ontology termp-valuen
integument3.96e-1346
integumental system3.96e-1346
adipose tissue3.39e-1114
skin of body2.48e-1041
trunk8.21e-09199
mesenchyme4.21e-08160
entire embryonic mesenchyme4.21e-08160
body cavity or lining3.58e-0749
articulation6.83e-078
skeletal joint6.83e-078
articular system6.83e-078


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)
MA0003.10.515118
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.12.02362
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
MA0055.10.0586456
MA0056.10
MA0057.12.74001
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.12.43863
MA0069.11.02175
MA0070.12.30704
MA0071.10.625297
MA0072.11.00572
MA0073.153.0108
MA0074.13.89731
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
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
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.314898
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
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.569061
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.22.25875
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.132326
MA0155.14.31015
MA0156.10.417278
MA0157.11.89858
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.13.59546
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.49373
MA0102.21.58513
MA0258.10.788656
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
CTCF#1066443.573504248716680.01316635007238510.0466002587505026
SUZ12#23512216.70526030368760.005660234682079570.0255587898292926



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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