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Coexpression cluster:C1856: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,2.22212,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,2.31449,1.50573,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,1.54297,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,0.758594,0.417272,0.195238,1.06371,0.654459,1.00769,0.301779,0.415749,0.580638,0.132849,0.451846,1.74542,1.32072,1.74151,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,2.44935,1.2359,0.724351,0.4631,2.77586,0.233662,0.688844,1.04369,2.92501,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,1.05625,1.23387,0.741483,0.709554,0.240727,0.917983,0.987729,0.543014,1.44891,0.934302,0.755403,0.327263,1.18161,0.0719601,2.9256,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,1.35434,1.11542,3.24765,1.05402,0.494368,0.631235,1.37132,0.412056,2.6759,2.47721,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,3.075,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,0.443702
|tfbs_overrepresentation_for_novel_motifs=0.508327,2.22212,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,2.31449,1.50573,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,1.54297,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,0.758594,0.417272,0.195238,1.06371,0.654459,1.00769,0.301779,0.415749,0.580638,0.132849,0.451846,1.74542,1.32072,1.74151,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,2.44935,1.2359,0.724351,0.4631,2.77586,0.233662,0.688844,1.04369,2.92501,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,1.05625,1.23387,0.741483,0.709554,0.240727,0.917983,0.987729,0.543014,1.44891,0.934302,0.755403,0.327263,1.18161,0.0719601,2.9256,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,1.35434,1.11542,3.24765,1.05402,0.494368,0.631235,1.37132,0.412056,2.6759,2.47721,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,3.075,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,0.443702
|tfbs_overrepresentation_jaspar=MA0003.1;1.80249,MA0004.1;0.626788,MA0006.1;0.452993,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;2.31153,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;1.01397,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;4.57459,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;1.65981,MA0072.1;2.45107,MA0073.1;2.92967,MA0074.1;1.73427,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;0.412364,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;1.16366,MA0103.1;0.442769,MA0105.1;1.58771,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;0.277033,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;0.0359558,MA0147.1;0.386018,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;0.83106,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.77901,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.21472,MA0163.1;1.99104,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.94612,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:14, 22 January 2013


Full id: C1856_brain_parietal_temporal_occipital_duodenum_Fibroblast_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr1:34286163..34286166,-p@chr1:34286163..34286166
-
Hg19::chr1:34630742..34630755,-p3@CSMD2
Hg19::chr1:34630758..34630772,-p2@CSMD2
Hg19::chr1:34630820..34630844,-p1@CSMD2
Hg19::chr1:34630978..34630987,-p5@CSMD2


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
skin fibroblast8.99e-1023
fibroblast7.75e-0776
Uber Anatomy
Ontology termp-valuen
central nervous system3.31e-3581
neural tube4.87e-3556
neural rod4.87e-3556
future spinal cord4.87e-3556
neural keel4.87e-3556
nervous system6.81e-3489
regional part of nervous system1.29e-3253
regional part of brain1.29e-3253
neurectoderm4.07e-2986
brain3.51e-2868
future brain3.51e-2868
neural plate5.94e-2882
presumptive neural plate5.94e-2882
brain grey matter7.86e-2734
gray matter7.86e-2734
regional part of forebrain1.36e-2641
forebrain1.36e-2641
anterior neural tube1.36e-2641
future forebrain1.36e-2641
telencephalon2.45e-2634
cerebral hemisphere3.58e-2532
regional part of telencephalon6.03e-2532
structure with developmental contribution from neural crest1.08e-21132
ecto-epithelium3.90e-21104
pre-chordal neural plate4.77e-2161
ectoderm-derived structure3.31e-20171
ectoderm3.31e-20171
presumptive ectoderm3.31e-20171
cerebral cortex7.65e-2025
pallium7.65e-2025
neocortex2.50e-1820
regional part of cerebral cortex6.30e-1822
adult organism1.11e-14114
tube2.40e-12192
organ system subdivision1.54e-09223
posterior neural tube1.75e-0915
chordal neural plate1.75e-0915
multi-cellular organism5.95e-09656
anatomical conduit1.53e-08240
neural nucleus2.04e-089
nucleus of brain2.04e-089
integument3.66e-0846
integumental system3.66e-0846
segmental subdivision of nervous system4.73e-0813
basal ganglion5.59e-089
nuclear complex of neuraxis5.59e-089
aggregate regional part of brain5.59e-089
collection of basal ganglia5.59e-089
cerebral subcortex5.59e-089
organ part7.15e-08218
skin of body7.84e-0841
segmental subdivision of hindbrain3.01e-0712
hindbrain3.01e-0712
presumptive hindbrain3.01e-0712
gyrus7.68e-076


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)
MA0003.11.80249
MA0004.10.626788
MA0006.10.452993
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
MA0030.12.31153
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
MA0055.11.01397
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
MA0068.14.57459
MA0069.11.09737
MA0070.11.08584
MA0071.11.65981
MA0072.12.45107
MA0073.12.92967
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.11.58771
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
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.77901
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.11.99104
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.94612
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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#1066444.288205098460020.005152015588243280.0239376882294038
EP300#203345.419153380978560.00209386927943890.0121206969113912
TAF7#687936.859841642954350.005843286407019040.0262491715369548



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:C1856&oldid=2570367"