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Coexpression cluster:C1657: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,2.98939,0.621241,0.778743,0.752887,0.721271,0.453496,1.20439,0.963929,0.395009,1.42981,0.501863,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,1.68319,0.758594,0.417272,3.37137,1.87167,0.654459,0.388123,1.48009,0.415749,0.580638,0.414516,0.451846,1.25074,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,1.06581,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,1.66643,1.23387,2.09345,0.255232,0.675933,2.11876,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,2.19312,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,1.14173,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,0.951411,0.717647,2.32322,2.90764,0.512457,1.05402,0.494368,1.52665,1.37132,1.05995,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,1.7291,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,1.69829,0.526389,3.25206,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,2.49515,0.731946,1.45393
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,2.98939,0.621241,0.778743,0.752887,0.721271,0.453496,1.20439,0.963929,0.395009,1.42981,0.501863,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,1.68319,0.758594,0.417272,3.37137,1.87167,0.654459,0.388123,1.48009,0.415749,0.580638,0.414516,0.451846,1.25074,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,1.06581,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,1.66643,1.23387,2.09345,0.255232,0.675933,2.11876,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,2.19312,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,1.14173,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,0.951411,0.717647,2.32322,2.90764,0.512457,1.05402,0.494368,1.52665,1.37132,1.05995,1.00558,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.995523,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,1.7291,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,1.69829,0.526389,3.25206,1.15522,2.31232,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,2.49515,0.731946,1.45393
|tfbs_overrepresentation_jaspar=MA0003.1;1.40197,MA0004.1;0.626788,MA0006.1;2.00428,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,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;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;0.0853006,MA0056.1;0,MA0057.1;1.05691,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;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;2.08296,MA0074.1;0.730989,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;0.818263,MA0089.1;0,MA0090.1;1.36977,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;0.520776,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;0.759606,MA0140.1;1.65391,MA0141.1;0.520334,MA0142.1;2.10746,MA0143.1;3.11528,MA0144.1;0.356507,MA0145.1;0.868598,MA0146.1;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;1.41695,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.23503,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;1.83842,MA0099.2;0.699641,MA0079.2;4.3662,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.80881,MA0442.1;0
}}
}}

Revision as of 20:05, 22 January 2013


Full id: C1657_pineal_cerebellum_temporal_occipital_duodenum_middle_brain



Phase1 CAGE Peaks

Hg19::chr12:119419286..119419293,+p4@SRRM4
Hg19::chr12:119419294..119419308,+p2@SRRM4
Hg19::chr15:89147826..89147846,+p@chr15:89147826..89147846
+
Hg19::chr20:61808928..61808938,+p@chr20:61808928..61808938
+
Hg19::chr3:52001995..52002004,-p@chr3:52001995..52002004
-


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
neuronal stem cell2.52e-088
neuron2.80e-076
neuroblast2.80e-076
electrically signaling cell2.80e-076
Uber Anatomy
Ontology termp-valuen
central nervous system1.25e-9381
nervous system5.55e-9389
regional part of nervous system3.86e-9053
regional part of brain3.86e-9053
neural tube3.93e-8956
neural rod3.93e-8956
future spinal cord3.93e-8956
neural keel3.93e-8956
brain6.34e-8568
future brain6.34e-8568
regional part of forebrain3.39e-7741
forebrain3.39e-7741
anterior neural tube3.39e-7741
future forebrain3.39e-7741
brain grey matter3.76e-6834
gray matter3.76e-6834
telencephalon7.68e-6834
neural plate4.00e-6682
presumptive neural plate4.00e-6682
cerebral hemisphere1.90e-6332
regional part of telencephalon3.51e-6332
neurectoderm1.67e-6286
regional part of cerebral cortex1.61e-5822
pre-chordal neural plate2.80e-5861
neocortex9.69e-5320
ecto-epithelium6.30e-52104
cerebral cortex5.19e-5125
pallium5.19e-5125
ectoderm-derived structure9.14e-48171
ectoderm9.14e-48171
presumptive ectoderm9.14e-48171
adult organism3.85e-40114
structure with developmental contribution from neural crest1.75e-38132
organ system subdivision2.18e-36223
tube3.26e-20192
basal ganglion9.63e-199
nuclear complex of neuraxis9.63e-199
aggregate regional part of brain9.63e-199
collection of basal ganglia9.63e-199
cerebral subcortex9.63e-199
neural nucleus3.90e-189
nucleus of brain3.90e-189
anatomical cluster1.01e-17373
gyrus1.13e-176
limbic system2.29e-155
temporal lobe3.17e-156
occipital lobe3.87e-155
parietal lobe6.89e-155
segmental subdivision of hindbrain3.84e-1412
hindbrain3.84e-1412
presumptive hindbrain3.84e-1412
posterior neural tube5.40e-1415
chordal neural plate5.40e-1415
anatomical conduit7.28e-14240
telencephalic nucleus2.12e-137
organ part2.90e-13218
segmental subdivision of nervous system6.09e-1313
gland of diencephalon6.73e-134
neuroendocrine gland6.73e-134
regional part of metencephalon2.18e-119
metencephalon2.18e-119
future metencephalon2.18e-119
epithelium4.10e-11306
brainstem4.78e-116
cell layer6.85e-11309
diencephalon1.13e-107
future diencephalon1.13e-107
frontal cortex7.11e-103
multi-tissue structure2.47e-09342
pons8.44e-093
germ layer6.38e-08560
germ layer / neural crest6.38e-08560
embryonic tissue6.38e-08560
presumptive structure6.38e-08560
germ layer / neural crest derived structure6.38e-08560
epiblast (generic)6.38e-08560
embryonic structure9.29e-08564
pineal body1.66e-072
regional part of epithalamus1.66e-072
secretory circumventricular organ1.66e-072
circumventricular organ1.66e-072
epithalamus1.66e-072
regional part of diencephalon2.21e-074
Ammon's horn2.25e-072
lobe parts of cerebral cortex2.25e-072
hippocampal formation2.25e-072
limbic lobe2.25e-072
middle temporal gyrus3.04e-072
amygdala3.04e-072
embryo3.14e-07592
middle frontal gyrus3.33e-072
developing anatomical structure4.33e-07581
pituitary gland4.61e-072
corpus striatum6.87e-074
striatum6.87e-074
ventral part of telencephalon6.87e-074


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
MA0006.12.00428
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
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
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.08296
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
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
MA0139.10.759606
MA0140.11.65391
MA0141.10.520334
MA0142.12.10746
MA0143.13.11528
MA0144.10.356507
MA0145.10.868598
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.23503
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.21.83842
MA0099.20.699641
MA0079.24.3662
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
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
CTBP2#1488225.08680013573130.002461438599678380.0138447967423422
POU5F1#54602134.1756805807628.81868530743257e-050.00130141963377554
REST#597835.790017229676810.009468788694433940.0356904440038251



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:C1657&oldid=2570168"