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Coexpression cluster:C1784: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,3.45852,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,2.11893,0.721271,0.453496,0.478935,0.963929,0.395009,2.18893,0.501863,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,2.28955,1.68319,0.27659,0.417272,0.195238,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.821929,0.451846,0.824538,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,2.94495,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.914416,2.9256,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,1.70662,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,1.05995,0.285668,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,2.60032,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.398598,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,2.39025
|tfbs_overrepresentation_for_novel_motifs=0.508327,3.45852,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,2.11893,0.721271,0.453496,0.478935,0.963929,0.395009,2.18893,0.501863,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,2.28955,1.68319,0.27659,0.417272,0.195238,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.821929,0.451846,0.824538,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,2.94495,1.69665,0.991065,1.53343,0.566575,0.330474,0.554326,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.914416,2.9256,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.780629,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,1.70662,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,1.05995,0.285668,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,2.60032,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.398598,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,2.39025
|tfbs_overrepresentation_jaspar=MA0003.1;4.3611,MA0004.1;1.51734,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.369468,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;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;1.48719,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;2.69304,MA0056.1;0,MA0057.1;1.05691,MA0058.1;1.29981,MA0059.1;1.29682,MA0060.1;1.55172,MA0061.1;1.44118,MA0063.1;0,MA0066.1;7.09348,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;12.1857,MA0074.1;1.73427,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;1.92154,MA0089.1;0,MA0090.1;1.36977,MA0091.1;0.629594,MA0092.1;1.43794,MA0093.1;1.15584,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;3.82415,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;2.60288,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;1.39016,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.868598,MA0146.1;0.946108,MA0147.1;1.00307,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;2.38271,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;3.37937,MA0065.2;2.73531,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;1.57192,MA0155.1;5.79564,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.21472,MA0163.1;8.36627,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;1.53298,MA0102.2;1.66336,MA0258.1;2.47453,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:11, 22 January 2013


Full id: C1784_heart_skeletal_left_tongue_diaphragm_cerebellum_temporal



Phase1 CAGE Peaks

Hg19::chr17:48172695..48172780,+p1@PDK2
Hg19::chr19:35629684..35629701,+p3@FXYD1
Hg19::chr19:35629702..35629742,+p1@FXYD1
Hg19::chr19:35629748..35629760,+p2@FXYD1
Hg19::chr19:35630028..35630083,+p7@FXYD1


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

GO IDGO nameFDR corrected p-value
GO:0004740pyruvate dehydrogenase (acetyl-transferring) kinase activity0.0192090723048097
GO:0018106peptidyl-histidine phosphorylation0.0192090723048097
GO:0018202peptidyl-histidine modification0.0192090723048097
GO:0004673protein histidine kinase activity0.0335181977945929
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0335181977945929
GO:0043168anion binding0.0448719349502542
GO:0031404chloride ion binding0.0448719349502542



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
fat cell5.61e-0815
Uber Anatomy
Ontology termp-valuen
adult organism1.10e-65114
neural tube1.68e-3256
neural rod1.68e-3256
future spinal cord1.68e-3256
neural keel1.68e-3256
regional part of nervous system6.36e-3053
regional part of brain6.36e-3053
neural plate2.43e-2682
presumptive neural plate2.43e-2682
brain4.81e-2568
future brain4.81e-2568
neurectoderm5.57e-2486
central nervous system1.25e-2381
regional part of forebrain3.18e-2341
forebrain3.18e-2341
anterior neural tube3.18e-2341
future forebrain3.18e-2341
organ system subdivision7.12e-21223
nervous system1.13e-2089
brain grey matter2.30e-1934
gray matter2.30e-1934
telencephalon2.30e-1934
structure with developmental contribution from neural crest2.80e-19132
ecto-epithelium6.07e-19104
cerebral hemisphere7.21e-1832
regional part of telencephalon8.03e-1832
multi-tissue structure6.03e-16342
regional part of cerebral cortex2.55e-1522
pre-chordal neural plate5.25e-1561
neocortex9.15e-1420
anatomical cluster5.22e-13373
ectoderm-derived structure1.52e-12171
ectoderm1.52e-12171
presumptive ectoderm1.52e-12171
cerebral cortex1.58e-1225
pallium1.58e-1225
organ4.96e-12503
anatomical conduit2.67e-11240
multi-cellular organism4.09e-11656
tube1.09e-10192
posterior neural tube2.36e-1015
chordal neural plate2.36e-1015
epithelium1.47e-09306
cell layer2.03e-09309
tissue3.78e-09773
anatomical system5.99e-09624
basal ganglion7.00e-099
nuclear complex of neuraxis7.00e-099
aggregate regional part of brain7.00e-099
collection of basal ganglia7.00e-099
cerebral subcortex7.00e-099
anatomical group7.70e-09625
neural nucleus1.08e-089
nucleus of brain1.08e-089
segmental subdivision of nervous system2.39e-0813
segmental subdivision of hindbrain6.78e-0812
hindbrain6.78e-0812
presumptive hindbrain6.78e-0812
organ part1.81e-07218
telencephalic nucleus4.06e-077


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)
MA0003.14.3611
MA0004.11.51734
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
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
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.11.48719
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.12.69304
MA0056.10
MA0057.11.05691
MA0058.11.29981
MA0059.11.29682
MA0060.11.55172
MA0061.11.44118
MA0063.10
MA0066.17.09348
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.112.1857
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.11.43794
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.13.82415
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.12.60288
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
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.10.946108
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.38271
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.23.37937
MA0065.22.73531
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.11.57192
MA0155.15.79564
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.18.36627
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.53298
MA0102.21.66336
MA0258.12.47453
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
HNF4A#3172313.87937421777220.0007561408847434270.0059452381135074



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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