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Coexpression cluster:C604: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.172755,0.725063,0.167518,0.277483,0.847893,0.757608,0.338925,0.0682671,0.510737,0.315942,0.252096,0.3759,0.177832,0.877494,0.137951,0.911078,0.534852,0.692936,0.431744,0.587627,0.501333,0.379112,0.26993,0.135481,0.200668,0.395548,0.9801,0.739386,0.140919,0.131814,0.662646,0.568576,1.01289,0.405736,0.116543,0.199172,0.114552,0.27709,0.675484,0.212026,0.745946,0.222502,0.118046,0.136946,0.24229,0.554944,0.339845,0.243586,0.394038,0.141004,0.407934,0.349819,0.224172,0.639823,0.784252,0.331716,0.143846,0.821863,0.896459,0.303639,0.606437,0.341844,0.0672442,0.509653,0.357077,0.478604,0.869007,1.22829,0.559029,1.06908,0.212516,0.249409,0.0195984,0.782342,0.0450471,0.357608,0.0348214,1.23743,1.36852,0.570606,0.443974,0.50868,0.356776,0.0697103,0.733386,0.00154893,0.0669348,0.550078,0.430803,1.32629,0.95934,0.70782,0.584068,0.0892066,0.139351,0.320157,0.427968,0.623577,0.434875,1.14976,2.25552,0.578851,0.618385,0.538198,1.18153,0.248535,0.523764,0.871038,0.581061,0.128402,0.175484,0.61581,0.49168,0.259545,0.912801,0.364707,0.0149922,1.91084,0.476505,0.630394,0.77444,0.428661,0.273941,0.366411,1.02031,0.495057,0.33358,0.588683,0.815183,0.0973529,0.708473,0.667822,0.828971,0.363559,0.971853,0.118371,0.230408,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,1.50374,0.469857,0.806155,0.454976,1.61933,0.627312,0.294496,0.943814,0.00708394,0.708834,0.844164,0.341434,1.09904,1.06976,0.808193,0.200711,0.179634,0.893382,0.691354,0.555323,1.02668,0.48429,0.356103,0.0806293,0.337803,0.162843
|tfbs_overrepresentation_for_novel_motifs=0.172755,0.725063,0.167518,0.277483,0.847893,0.757608,0.338925,0.0682671,0.510737,0.315942,0.252096,0.3759,0.177832,0.877494,0.137951,0.911078,0.534852,0.692936,0.431744,0.587627,0.501333,0.379112,0.26993,0.135481,0.200668,0.395548,0.9801,0.739386,0.140919,0.131814,0.662646,0.568576,1.01289,0.405736,0.116543,0.199172,0.114552,0.27709,0.675484,0.212026,0.745946,0.222502,0.118046,0.136946,0.24229,0.554944,0.339845,0.243586,0.394038,0.141004,0.407934,0.349819,0.224172,0.639823,0.784252,0.331716,0.143846,0.821863,0.896459,0.303639,0.606437,0.341844,0.0672442,0.509653,0.357077,0.478604,0.869007,1.22829,0.559029,1.06908,0.212516,0.249409,0.0195984,0.782342,0.0450471,0.357608,0.0348214,1.23743,1.36852,0.570606,0.443974,0.50868,0.356776,0.0697103,0.733386,0.00154893,0.0669348,0.550078,0.430803,1.32629,0.95934,0.70782,0.584068,0.0892066,0.139351,0.320157,0.427968,0.623577,0.434875,1.14976,2.25552,0.578851,0.618385,0.538198,1.18153,0.248535,0.523764,0.871038,0.581061,0.128402,0.175484,0.61581,0.49168,0.259545,0.912801,0.364707,0.0149922,1.91084,0.476505,0.630394,0.77444,0.428661,0.273941,0.366411,1.02031,0.495057,0.33358,0.588683,0.815183,0.0973529,0.708473,0.667822,0.828971,0.363559,0.971853,0.118371,0.230408,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,1.50374,0.469857,0.806155,0.454976,1.61933,0.627312,0.294496,0.943814,0.00708394,0.708834,0.844164,0.341434,1.09904,1.06976,0.808193,0.200711,0.179634,0.893382,0.691354,0.555323,1.02668,0.48429,0.356103,0.0806293,0.337803,0.162843
|tfbs_overrepresentation_jaspar=MA0003.1;0.0289908,MA0004.1;0.256222,MA0006.1;0.426713,MA0007.1;0.67744,MA0009.1;0.669377,MA0014.1;0.0332175,MA0017.1;0.494446,MA0019.1;0.990457,MA0024.1;0.570967,MA0025.1;0.796882,MA0027.1;2.25966,MA0028.1;0.148561,MA0029.1;0.588958,MA0030.1;0.578277,MA0031.1;0.518602,MA0038.1;0.34128,MA0040.1;0.594421,MA0041.1;0.746198,MA0042.1;0.687159,MA0043.1;0.669676,MA0046.1;0.659066,MA0048.1;0.23222,MA0050.1;0.246257,MA0051.1;0.337676,MA0052.1;0.598036,MA0055.1;0.120131,MA0056.1;0,MA0057.1;0.0873069,MA0058.1;0.182945,MA0059.1;0.182001,MA0060.1;0.0671843,MA0061.1;0.0537738,MA0063.1;0,MA0066.1;4.38042,MA0067.1;0.975379,MA0068.1;0.0373092,MA0069.1;1.57719,MA0070.1;0.644843,MA0071.1;5.14777,MA0072.1;0.640598,MA0073.1;9.46466e-07,MA0074.1;1.60579,MA0076.1;0.194691,MA0077.1;0.633326,MA0078.1;1.08632,MA0081.1;1.02736,MA0083.1;0.676499,MA0084.1;1.15904,MA0087.1;0.63829,MA0088.1;0.0411204,MA0089.1;0,MA0090.1;1.12017,MA0091.1;0.258318,MA0092.1;0.647316,MA0093.1;0.139688,MA0095.1;0,MA0098.1;0,MA0100.1;2.51026,MA0101.1;0.141917,MA0103.1;0.411001,MA0105.1;0.0162551,MA0106.1;0.37688,MA0107.1;0.0950422,MA0108.2;0.515791,MA0109.1;0,MA0111.1;0.617603,MA0113.1;0.39123,MA0114.1;0.636237,MA0115.1;4.91533,MA0116.1;0.320986,MA0117.1;0.705104,MA0119.1;0.170362,MA0122.1;0.729811,MA0124.1;0.860724,MA0125.1;0.779672,MA0130.1;0,MA0131.1;0.440395,MA0132.1;0,MA0133.1;0,MA0135.1;0.698212,MA0136.1;0.347318,MA0139.1;0.0481205,MA0140.1;0.30631,MA0141.1;2.30159,MA0142.1;0.489543,MA0143.1;1.79503,MA0144.1;0.0838502,MA0145.1;0.278475,MA0146.1;0.0247789,MA0147.1;0.326612,MA0148.1;0.758022,MA0149.1;0.298252,MA0062.2;0.191053,MA0035.2;0.305721,MA0039.2;0.000598337,MA0138.2;0.425279,MA0002.2;0.0612545,MA0137.2;0.153033,MA0104.2;0.0667907,MA0047.2;0.959769,MA0112.2;0.988185,MA0065.2;0.0514203,MA0150.1;0.201098,MA0151.1;0,MA0152.1;0.311809,MA0153.1;0.763487,MA0154.1;0.367546,MA0155.1;0.0403226,MA0156.1;0.469333,MA0157.1;0.46471,MA0158.1;0,MA0159.1;0.327637,MA0160.1;0.786431,MA0161.1;0,MA0162.1;0.0065085,MA0163.1;0.0031263,MA0164.1;0.402162,MA0080.2;0.139746,MA0018.2;0.98566,MA0099.2;0.312108,MA0079.2;5.17282e-08,MA0102.2;1.1957,MA0258.1;2.59112,MA0259.1;0.693919,MA0442.1;0
}}
}}

Revision as of 19:18, 22 January 2013


Full id: C604_Fibroblast_hepatic_Ewing_Preadipocyte_Smooth_Adipocyte_Olfactory



Phase1 CAGE Peaks

Hg19::chr2:3998213..3998216,+p@chr2:3998213..3998216
+
Hg19::chr6:169616396..169616409,-p@chr6:169616396..169616409
-
Hg19::chr6:169616977..169617034,-p@chr6:169616977..169617034
-
Hg19::chr6:169617543..169617560,-p@chr6:169617543..169617560
-
Hg19::chr6:169620344..169620364,-p@chr6:169620344..169620364
-
Hg19::chr6:169620383..169620394,-p@chr6:169620383..169620394
-
Hg19::chr6:169622388..169622400,-p@chr6:169622388..169622400
-
Hg19::chr6:169625268..169625291,-p@chr6:169625268..169625291
-
Hg19::chr6:169625328..169625341,-p@chr6:169625328..169625341
-
Hg19::chr6:169625418..169625430,-p@chr6:169625418..169625430
-
Hg19::chr6:169646344..169646377,-p@chr6:169646344..169646377
-
Hg19::chr6:169648866..169648879,-p4@THBS2
Hg19::chr6:169648933..169648983,-p2@THBS2
Hg19::chr6:169648975..169649020,+p@chr6:169648975..169649020
+
Hg19::chr6:169653931..169653949,-p1@THBS2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue6.95e-1262
striated muscle tissue6.95e-1262
myotome6.95e-1262
muscle tissue3.65e-1164
musculature3.65e-1164
musculature of body3.65e-1164
systemic artery4.01e-1133
systemic arterial system4.01e-1133
dense mesenchyme tissue1.12e-1073
somite2.13e-1071
presomitic mesoderm2.13e-1071
presumptive segmental plate2.13e-1071
dermomyotome2.13e-1071
trunk paraxial mesoderm2.13e-1071
paraxial mesoderm4.26e-1072
presumptive paraxial mesoderm4.26e-1072
integument4.87e-1046
integumental system4.87e-1046
multilaminar epithelium7.35e-1083
artery8.79e-1042
arterial blood vessel8.79e-1042
arterial system8.79e-1042
surface structure5.17e-0999
splanchnic layer of lateral plate mesoderm1.60e-0883
epithelial vesicle1.74e-0878
omentum2.08e-086
peritoneum2.08e-086
abdominal cavity2.08e-086
visceral peritoneum2.08e-086
skin of body3.37e-0841
epithelial tube open at both ends8.02e-0859
blood vessel8.02e-0859
blood vasculature8.02e-0859
vascular cord8.02e-0859
adipose tissue1.43e-0714
heart2.55e-0724
primitive heart tube2.55e-0724
primary heart field2.55e-0724
anterior lateral plate mesoderm2.55e-0724
heart tube2.55e-0724
heart primordium2.55e-0724
cardiac mesoderm2.55e-0724
cardiogenic plate2.55e-0724
heart rudiment2.55e-0724
blood vessel layer3.34e-077
vasculature3.57e-0778
vascular system3.57e-0778
cardiovascular system7.87e-07109
female gonad8.84e-0713
Disease
Ontology termp-valuen
ovarian cancer1.92e-1214


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)
MA0003.10.0289908
MA0004.10.256222
MA0006.10.426713
MA0007.10.67744
MA0009.10.669377
MA0014.10.0332175
MA0017.10.494446
MA0019.10.990457
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.746198
MA0042.10.687159
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.120131
MA0056.10
MA0057.10.0873069
MA0058.10.182945
MA0059.10.182001
MA0060.10.0671843
MA0061.10.0537738
MA0063.10
MA0066.14.38042
MA0067.10.975379
MA0068.10.0373092
MA0069.11.57719
MA0070.10.644843
MA0071.15.14777
MA0072.10.640598
MA0073.19.46466e-07
MA0074.11.60579
MA0076.10.194691
MA0077.10.633326
MA0078.11.08632
MA0081.11.02736
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.0411204
MA0089.10
MA0090.11.12017
MA0091.10.258318
MA0092.10.647316
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.12.51026
MA0101.10.141917
MA0103.10.411001
MA0105.10.0162551
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.617603
MA0113.10.39123
MA0114.10.636237
MA0115.14.91533
MA0116.10.320986
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.12.30159
MA0142.10.489543
MA0143.11.79503
MA0144.10.0838502
MA0145.10.278475
MA0146.10.0247789
MA0147.10.326612
MA0148.10.758022
MA0149.10.298252
MA0062.20.191053
MA0035.20.305721
MA0039.20.000598337
MA0138.20.425279
MA0002.20.0612545
MA0137.20.153033
MA0104.20.0667907
MA0047.20.959769
MA0112.20.988185
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.367546
MA0155.10.0403226
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.327637
MA0160.10.786431
MA0161.10
MA0162.10.0065085
MA0163.10.0031263
MA0164.10.402162
MA0080.20.139746
MA0018.20.98566
MA0099.20.312108
MA0079.25.17282e-08
MA0102.21.1957
MA0258.12.59112
MA0259.10.693919
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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