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Coexpression cluster:C1918: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.26722,5.63132,0.500341,0.654974,2.01096,0.653236,1.73914,0.324142,0.321368,0.345702,0.621241,0.778743,0.752887,1.71413,0.453496,0.478935,0.963929,1.02276,4.95664,0.969147,0.500405,0.384437,0.645033,0.44943,1.35492,0.802434,1.29435,0.642741,0.458349,0.659743,0.598009,1.00172,0.94379,1.38854,0.417272,1.1597,0.413782,0.654459,0.388123,0.301779,0.415749,1.42042,0.132849,0.451846,0.824538,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,1.64682,2.37491,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,2.26785,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.49825,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,1.78691,2.68381,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,3.19738,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,2.39025
|tfbs_overrepresentation_for_novel_motifs=1.26722,5.63132,0.500341,0.654974,2.01096,0.653236,1.73914,0.324142,0.321368,0.345702,0.621241,0.778743,0.752887,1.71413,0.453496,0.478935,0.963929,1.02276,4.95664,0.969147,0.500405,0.384437,0.645033,0.44943,1.35492,0.802434,1.29435,0.642741,0.458349,0.659743,0.598009,1.00172,0.94379,1.38854,0.417272,1.1597,0.413782,0.654459,0.388123,0.301779,0.415749,1.42042,0.132849,0.451846,0.824538,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,1.64682,2.37491,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,2.26785,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.49825,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,1.78691,2.68381,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,3.19738,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,2.39025
|tfbs_overrepresentation_jaspar=MA0003.1;0.136928,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.660087,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,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;1.7452,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;1.7027,MA0050.1;0.613347,MA0051.1;1.73592,MA0052.1;1.03442,MA0055.1;4.0988,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;6.60095,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.0140295,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;2.53033,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,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;0.175503,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;4.85446,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;2.33916,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;1.96224,MA0065.2;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;2.98611,MA0155.1;1.91168,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;0.0439995,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;0.345771,MA0259.1;2.71109,MA0442.1;0
}}
}}

Revision as of 20:17, 22 January 2013


Full id: C1918_smooth_leiomyoma_bladder_Mesenchymal_cervix_esophagus_prostate



Phase1 CAGE Peaks

Hg19::chr3:123419560..123419573,-p26@MYLK
Hg19::chr3:123419588..123419611,-p15@MYLK
Hg19::chr3:123419651..123419676,-p8@MYLK
Hg19::chr3:123419683..123419705,-p17@MYLK
Hg19::chr3:123419964..123419975,-p13@MYLK


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.08e-66114
regional part of nervous system1.99e-3053
regional part of brain1.99e-3053
neural tube6.99e-3056
neural rod6.99e-3056
future spinal cord6.99e-3056
neural keel6.99e-3056
brain grey matter8.15e-2834
gray matter8.15e-2834
telencephalon1.73e-2734
regional part of forebrain3.25e-2741
forebrain3.25e-2741
anterior neural tube3.25e-2741
future forebrain3.25e-2741
cerebral hemisphere1.59e-2532
regional part of telencephalon3.36e-2532
brain4.85e-2268
future brain4.85e-2268
neural plate2.14e-2182
presumptive neural plate2.14e-2182
central nervous system4.15e-2081
regional part of cerebral cortex8.09e-2022
neurectoderm8.49e-2086
nervous system6.70e-1889
pre-chordal neural plate9.96e-1861
neocortex2.82e-1720
cerebral cortex7.80e-1725
pallium7.80e-1725
ecto-epithelium3.35e-14104
basal ganglion2.18e-139
nuclear complex of neuraxis2.18e-139
aggregate regional part of brain2.18e-139
collection of basal ganglia2.18e-139
cerebral subcortex2.18e-139
neural nucleus2.53e-139
nucleus of brain2.53e-139
organ system subdivision6.39e-13223
structure with developmental contribution from neural crest6.22e-12132
reproductive organ4.84e-1148
organ1.31e-10503
telencephalic nucleus1.40e-107
reproductive structure1.52e-1059
reproductive system1.52e-1059
ectoderm-derived structure1.03e-09171
ectoderm1.03e-09171
presumptive ectoderm1.03e-09171
body cavity1.93e-0946
anatomical cavity4.66e-0961
gyrus6.26e-096
limbic system1.51e-085
brainstem1.57e-086
body cavity or lining1.66e-0849
anatomical conduit2.56e-08240
omentum3.11e-086
peritoneum3.11e-086
abdominal cavity3.11e-086
visceral peritoneum3.11e-086
body cavity precursor3.57e-0854
organ part3.85e-08218
female reproductive organ1.32e-0737
female reproductive system1.32e-0737
tube1.55e-07192
anatomical cluster1.94e-07373
multi-tissue structure2.63e-07342
multi-cellular organism3.39e-07656
embryonic structure3.62e-07564
corpus striatum4.35e-074
striatum4.35e-074
ventral part of telencephalon4.35e-074
future corpus striatum4.35e-074
right ovary5.30e-075
anatomical system5.77e-07624
germ layer6.05e-07560
germ layer / neural crest6.05e-07560
embryonic tissue6.05e-07560
presumptive structure6.05e-07560
germ layer / neural crest derived structure6.05e-07560
epiblast (generic)6.05e-07560
developing anatomical structure6.14e-07581
anatomical group6.61e-07625


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)
MA0003.10.136928
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.7027
MA0050.10.613347
MA0051.11.73592
MA0052.11.03442
MA0055.14.0988
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.16.60095
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.12.53033
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
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
MA0105.10.175503
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
MA0139.14.85446
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.12.33916
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.21.96224
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.98611
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.27276
MA0102.21.66336
MA0258.10.345771
MA0259.12.71109
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1918&oldid=2570429"