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Coexpression cluster:C2019: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,1.68128,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,1.16078,0.621241,0.778743,2.94938,0.721271,2.00597,1.20439,0.963929,0.395009,3.96549,1.54297,0.500405,3.1828,0.645033,0.44943,1.35492,0.802434,1.29435,0.642741,1.16016,1.90917,0.598009,1.00172,0.359091,2.96574,1.88355,0.757784,0.413782,2.66282,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,5.78212,0.533483,0.734485,0.609718,0.785708,0.458489,0.817229,0.746838,2.38257,1.08035,1.2359,0.724351,0.4631,1.64902,0.659455,0.688844,1.04369,0.736968,1.55219,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.741483,0.255232,2.72671,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.166306,1.88098,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.780629,1.06255,3.27673,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,1.27602,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,14.4098
|tfbs_overrepresentation_for_novel_motifs=0.508327,1.68128,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,1.16078,0.621241,0.778743,2.94938,0.721271,2.00597,1.20439,0.963929,0.395009,3.96549,1.54297,0.500405,3.1828,0.645033,0.44943,1.35492,0.802434,1.29435,0.642741,1.16016,1.90917,0.598009,1.00172,0.359091,2.96574,1.88355,0.757784,0.413782,2.66282,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,5.78212,0.533483,0.734485,0.609718,0.785708,0.458489,0.817229,0.746838,2.38257,1.08035,1.2359,0.724351,0.4631,1.64902,0.659455,0.688844,1.04369,0.736968,1.55219,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.741483,0.255232,2.72671,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.166306,1.88098,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.780629,1.06255,3.27673,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,1.27602,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,14.4098
|tfbs_overrepresentation_jaspar=MA0003.1;1.40197,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.369468,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;2.29497,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.860776,MA0061.1;0.791444,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.0469445,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;4.10406,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;5.61073,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;2.96863,MA0140.1;4.03435,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;3.46016,MA0146.1;0.6031,MA0147.1;1.00307,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.311551,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;8.80608,MA0065.2;5.1727,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;6.71259,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.00463,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;1.49262,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;1.27276,MA0102.2;1.66336,MA0258.1;4.41151,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:21, 22 January 2013


Full id: C2019_mature_sacrococcigeal_gastric_Adipocyte_Synoviocyte_Mesenchymal_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr9:129884902..129884922,-p1@ANGPTL2
Hg19::chr9:129884924..129884937,-p3@ANGPTL2
Hg19::chr9:129884944..129884979,-p2@ANGPTL2
Hg19::chr9:129884994..129885007,-p4@ANGPTL2
Hg19::chr9:129885010..129885017,-p5@ANGPTL2


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
fibroblast3.64e-1376
non-terminally differentiated cell1.58e-12106
fat cell5.14e-1115
mesodermal cell7.41e-09121
muscle precursor cell2.22e-0858
myoblast2.22e-0858
multi-potent skeletal muscle stem cell2.22e-0858
contractile cell2.82e-0859
muscle cell4.73e-0855
electrically responsive cell4.75e-0861
electrically active cell4.75e-0861
Uber Anatomy
Ontology termp-valuen
anatomical cluster6.97e-12373
multi-cellular organism1.74e-11656
epithelium4.03e-11306
cell layer4.94e-11309
muscle tissue2.10e-1064
musculature2.10e-1064
musculature of body2.10e-1064
dense mesenchyme tissue2.39e-1073
splanchnic layer of lateral plate mesoderm3.85e-1083
adult organism4.46e-10114
somite6.47e-1071
presomitic mesoderm6.47e-1071
presumptive segmental plate6.47e-1071
dermomyotome6.47e-1071
trunk paraxial mesoderm6.47e-1071
epithelial vesicle6.73e-1078
paraxial mesoderm6.75e-1072
presumptive paraxial mesoderm6.75e-1072
skeletal muscle tissue8.72e-1062
striated muscle tissue8.72e-1062
myotome8.72e-1062
multi-tissue structure1.08e-09342
structure with developmental contribution from neural crest7.58e-09132
unilaminar epithelium1.12e-08148
anatomical system2.47e-08624
mesenchyme3.51e-08160
entire embryonic mesenchyme3.51e-08160
anatomical group3.75e-08625
trunk mesenchyme3.84e-08122
vasculature4.76e-0878
vascular system4.76e-0878
anatomical conduit5.86e-08240
primary circulatory organ1.12e-0727
adipose tissue1.18e-0714
multilaminar epithelium1.43e-0783
vessel3.44e-0768
epithelial tube open at both ends4.36e-0759
blood vessel4.36e-0759
blood vasculature4.36e-0759
vascular cord4.36e-0759
circulatory system5.68e-07112
epithelial tube6.27e-07117


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)
MA0003.11.40197
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.14.10406
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.15.61073
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.96863
MA0140.14.03435
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.13.46016
MA0146.10.6031
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.28.80608
MA0065.25.1727
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.16.71259
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.27276
MA0102.21.66336
MA0258.14.41151
MA0259.11.02361
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#1066455.360256373075030.0002259278299937090.00250325447026447
E2F6#187655.017155731697390.0003144978599297790.00323349497865782
HEY1#2346254.040111043105710.0009288852205177990.00675146798981547
MAX#414956.452555509007128.93743970843928e-050.00130859002622976
MYC#460955.22228187160940.0002573944848850610.00276877357162539
PAX5#507956.669565531177837.57493746384605e-050.00117185438273829
SPI1#668858.204323508522732.68916109982495e-050.000575873069724457
TAF1#687253.343046285745290.002394600090870310.0135586684136842
TAF7#6879511.43306940492395.11611886715123e-060.000157617208957642
TBP#690853.706770687096390.001428755106721120.00920585813997454
TCF7L2#6934510.77017656313736.89693748574565e-060.000200308468874802
TFAP2A#7020516.5186343730458.12390055913032e-073.54555808815299e-05
TFAP2C#7022510.80922860986026.77323239348459e-060.000197594865347245
ZNF263#1012758.221841637010682.6606316672286e-050.000572817379290225



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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