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Coexpression cluster:C769: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.62403,MA0004.1;0.349539,MA0006.1;0.605586,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.79286,MA0017.1;0.24363,MA0019.1;0.486183,MA0024.1;0.688373,MA0025.1;0.921763,MA0027.1;2.39404,MA0028.1;0.224112,MA0029.1;0.707146,MA0030.1;0.696006,MA0031.1;0.633489,MA0038.1;0.443833,MA0040.1;0.712837,MA0041.1;0.366339,MA0042.1;0.337481,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;0.0494179,MA0050.1;0.897608,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;0.00989454,MA0056.1;0,MA0057.1;0.0465155,MA0058.1;0.265212,MA0059.1;0.2641,MA0060.1;0.119532,MA0061.1;0.100525,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;0.0758327,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;0.40788,MA0072.1;3.00023,MA0073.1;0.000309691,MA0074.1;0.439193,MA0076.1;0.278993,MA0077.1;0.753278,MA0078.1;2.27097,MA0081.1;0.26424,MA0083.1;0.79797,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;0.0234479,MA0089.1;0,MA0090.1;0.291627,MA0091.1;0.351901,MA0092.1;0.318032,MA0093.1;0.213288,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;0.216017,MA0103.1;0.203171,MA0105.1;0.0403209,MA0106.1;0.482519,MA0107.1;0.156959,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.303543,MA0113.1;0.498009,MA0114.1;0.465415,MA0115.1;1.02805,MA0116.1;0.159642,MA0117.1;0.827487,MA0119.1;0.250314,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;2.09043,MA0130.1;0,MA0131.1;1.3572,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.0922451,MA0140.1;1.84316,MA0141.1;0.2626,MA0142.1;0.602852,MA0143.1;0.498176,MA0144.1;0.142196,MA0145.1;0.277793,MA0146.1;0.0109959,MA0147.1;0.162359,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;1.04409,MA0039.2;0.000152622,MA0138.2;0.534556,MA0002.2;0.111226,MA0137.2;0.229531,MA0104.2;0.378829,MA0047.2;0.47109,MA0112.2;0.106997,MA0065.2;1.21559,MA0150.1;0.286461,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;0.0391503,MA0155.1;1.4993,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;0.162854,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.519336,MA0163.1;0.122012,MA0164.1;0.509774,MA0080.2;0.21336,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;0.239,MA0102.2;1.32663,MA0258.1;0.135061,MA0259.1;0.168926,MA0442.1;0
}}
}}

Revision as of 19:26, 22 January 2013


Full id: C769_Fibroblast_Sertoli_Smooth_Mesothelial_Preadipocyte_Adipocyte_hepatic



Phase1 CAGE Peaks

Hg19::chr3:124732018..124732029,-p15@HEG1
Hg19::chr3:124732162..124732179,-p9@HEG1
Hg19::chr3:124732278..124732290,-p11@HEG1
Hg19::chr3:124732327..124732338,-p10@HEG1
Hg19::chr3:124732396..124732408,-p6@HEG1
Hg19::chr3:124732564..124732581,-p3@HEG1
Hg19::chr3:124732593..124732604,-p13@HEG1
Hg19::chr3:124732713..124732735,-p2@HEG1
Hg19::chr3:124732820..124732831,-p8@HEG1
Hg19::chr3:124774831..124774852,-p1@HEG1
Hg19::chr3:124774870..124774877,-p4@HEG1


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
fibroblast8.89e-1576
mesodermal cell7.20e-10121
mesothelial cell1.41e-0819
smooth muscle cell9.14e-0843
smooth muscle myoblast9.14e-0843
muscle cell3.77e-0755
muscle precursor cell4.38e-0758
myoblast4.38e-0758
multi-potent skeletal muscle stem cell4.38e-0758
contractile cell9.30e-0759
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm3.05e-1183
circulatory system9.37e-09112
multi-cellular organism1.18e-08656
vasculature1.87e-0878
vascular system1.87e-0878
cardiovascular system2.47e-08109
anatomical system2.57e-08624
anatomical group4.47e-08625
epithelial tube6.31e-08117
primary circulatory organ9.21e-0827
heart2.27e-0724
primitive heart tube2.27e-0724
primary heart field2.27e-0724
anterior lateral plate mesoderm2.27e-0724
heart tube2.27e-0724
heart primordium2.27e-0724
cardiac mesoderm2.27e-0724
cardiogenic plate2.27e-0724
heart rudiment2.27e-0724
unilaminar epithelium2.52e-07148
cell layer2.87e-07309
epithelial tube open at both ends2.96e-0759
blood vessel2.96e-0759
blood vasculature2.96e-0759
vascular cord2.96e-0759
mesoderm5.43e-07315
mesoderm-derived structure5.43e-07315
presumptive mesoderm5.43e-07315
skeletal muscle tissue5.80e-0762
striated muscle tissue5.80e-0762
myotome5.80e-0762
epithelium5.88e-07306
organ component layer7.79e-0766
muscle tissue8.85e-0764
musculature8.85e-0764
musculature of body8.85e-0764


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)
MA0003.11.62403
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.10.79286
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.897608
MA0051.10.439895
MA0052.10.716602
MA0055.10.00989454
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.13.00023
MA0073.10.000309691
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.12.27097
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.12.09043
MA0130.10
MA0131.11.3572
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.11.84316
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.277793
MA0146.10.0109959
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.20.000152622
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.378829
MA0047.20.47109
MA0112.20.106997
MA0065.21.21559
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.11.4993
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.519336
MA0163.10.122012
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.239
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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

No analysis results for this cluster

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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