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Coexpression cluster:C961: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.83884,0.735382,0.305225,0.440628,0.267236,0.439064,0.511871,0.164003,0.94513,1.21683,0.410439,0.553754,4.04347,0.500805,0.266007,0.287179,0.728104,0.218596,0.137566,0.216842,0.305279,0.599077,0.431698,0.262652,0.347482,0.575764,0.36063,0.429643,0.270022,0.329945,0.389837,0.764231,0.190489,0.129565,0.23642,0.69854,1.90822,1.12093,0.213144,0.451713,0.235191,0.374544,0.160114,0.264644,0.301725,0.887061,0.51292,1.82528,0.340916,0.270138,0.589559,0.524278,0.546719,0.839846,0.99088,0.503626,0.752594,0.472204,0.67562,0.47124,0.804523,0.5152,0.162346,0.700946,1.31866,0.667267,1.07848,1.44489,0.754027,2.85992,1.69415,0.504216,0.0724994,0.988898,0.392686,1.21675,0.342172,1.63758,0.750836,0.341765,0.141333,0.699894,1.31794,0.498312,0.937974,0.182485,0.0591186,0.659731,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,2.08725,0.598862,0.423564,0.82268,0.619373,2.07548,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,0.0867932,0.388709,0.664981,0.577715,0.980696,0.612519,0.436445,2.30268,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,1.01734,1.03718,0.539846,1.18405,0.0922077,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,1.17257,0.641461,1.83907,0.37143,0.193834,0.0656964,0.977032,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.865335,0.673453,0.531409,0.183544,0.510589,0.0121205
|tfbs_overrepresentation_for_novel_motifs=0.83884,0.735382,0.305225,0.440628,0.267236,0.439064,0.511871,0.164003,0.94513,1.21683,0.410439,0.553754,4.04347,0.500805,0.266007,0.287179,0.728104,0.218596,0.137566,0.216842,0.305279,0.599077,0.431698,0.262652,0.347482,0.575764,0.36063,0.429643,0.270022,0.329945,0.389837,0.764231,0.190489,0.129565,0.23642,0.69854,1.90822,1.12093,0.213144,0.451713,0.235191,0.374544,0.160114,0.264644,0.301725,0.887061,0.51292,1.82528,0.340916,0.270138,0.589559,0.524278,0.546719,0.839846,0.99088,0.503626,0.752594,0.472204,0.67562,0.47124,0.804523,0.5152,0.162346,0.700946,1.31866,0.667267,1.07848,1.44489,0.754027,2.85992,1.69415,0.504216,0.0724994,0.988898,0.392686,1.21675,0.342172,1.63758,0.750836,0.341765,0.141333,0.699894,1.31794,0.498312,0.937974,0.182485,0.0591186,0.659731,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,2.08725,0.598862,0.423564,0.82268,0.619373,2.07548,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,0.0867932,0.388709,0.664981,0.577715,0.980696,0.612519,0.436445,2.30268,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,1.01734,1.03718,0.539846,1.18405,0.0922077,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,1.17257,0.641461,1.83907,0.37143,0.193834,0.0656964,0.977032,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.865335,0.673453,0.531409,0.183544,0.510589,0.0121205
|tfbs_overrepresentation_jaspar=MA0003.1;0.000472949,MA0004.1;0.415381,MA0006.1;0.733408,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.0956087,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;1.80828,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;3.04353,MA0031.1;1.69202,MA0038.1;0.514558,MA0040.1;1.8598,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.0764047,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;0.693769,MA0056.1;0,MA0057.1;0.539841,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;1.99244,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;0.0176541,MA0074.1;0.509711,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;0.158781,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.257174,MA0105.1;0.229733,MA0106.1;0.554855,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;0.322254,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;1.0529,MA0145.1;0.046841,MA0146.1;0.0045741,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.0006485,MA0138.2;0.608783,MA0002.2;0.46405,MA0137.2;1.42372,MA0104.2;0.161609,MA0047.2;1.34084,MA0112.2;0.0433683,MA0065.2;0.0483532,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;0.062786,MA0155.1;0.0402662,MA0156.1;0.288314,MA0157.1;1.57029,MA0158.1;0,MA0159.1;0.212043,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.14518,MA0163.1;0.216998,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.104637,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.624802,MA0442.1;0
}}
}}

Revision as of 19:35, 22 January 2013


Full id: C961_pineal_parietal_gastrointestinal_pons_pituitary_cerebellum_occipital



Phase1 CAGE Peaks

Hg19::chr8:31497019..31497036,+p24@NRG1
Hg19::chr8:31497051..31497081,+p11@NRG1
Hg19::chr8:31497083..31497101,+p13@NRG1
Hg19::chr8:31497277..31497285,+p29@NRG1
Hg19::chr8:31599997..31600000,+p@chr8:31599997..31600000
+
Hg19::chr8:31667277..31667281,+p@chr8:31667277..31667281
+
Hg19::chr8:32060728..32060732,+p@chr8:32060728..32060732
+
Hg19::chr8:32180390..32180392,+p@chr8:32180390..32180392
+
Hg19::chr8:32221614..32221617,+p@chr8:32221614..32221617
+


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
Merkel cell5.71e-072
Uber Anatomy
Ontology termp-valuen
neural tube4.85e-8956
neural rod4.85e-8956
future spinal cord4.85e-8956
neural keel4.85e-8956
regional part of nervous system1.80e-8553
regional part of brain1.80e-8553
central nervous system5.93e-6781
brain6.02e-6768
future brain6.02e-6768
nervous system2.27e-6589
regional part of forebrain1.06e-6441
forebrain1.06e-6441
anterior neural tube1.06e-6441
future forebrain1.06e-6441
neurectoderm1.62e-6386
neural plate1.04e-6082
presumptive neural plate1.04e-6082
brain grey matter5.56e-5934
gray matter5.56e-5934
cerebral hemisphere5.56e-5832
telencephalon2.94e-5434
regional part of telencephalon2.48e-5332
ecto-epithelium1.38e-50104
regional part of cerebral cortex1.36e-4522
pre-chordal neural plate5.91e-4461
cerebral cortex6.26e-4425
pallium6.26e-4425
neocortex8.14e-4020
ectoderm-derived structure2.54e-37171
ectoderm2.54e-37171
presumptive ectoderm2.54e-37171
structure with developmental contribution from neural crest1.22e-35132
adult organism2.47e-34114
organ system subdivision1.31e-24223
posterior neural tube3.67e-2415
chordal neural plate3.67e-2415
segmental subdivision of hindbrain5.45e-2112
hindbrain5.45e-2112
presumptive hindbrain5.45e-2112
tube4.85e-20192
segmental subdivision of nervous system3.12e-1913
brainstem3.65e-196
gyrus6.87e-196
neural nucleus3.77e-169
nucleus of brain3.77e-169
anatomical conduit5.99e-14240
regional part of metencephalon3.25e-139
metencephalon3.25e-139
future metencephalon3.25e-139
corpus striatum9.20e-134
striatum9.20e-134
ventral part of telencephalon9.20e-134
future corpus striatum9.20e-134
organ part2.54e-12218
anatomical cluster3.12e-12373
basal ganglion8.15e-129
nuclear complex of neuraxis8.15e-129
aggregate regional part of brain8.15e-129
collection of basal ganglia8.15e-129
cerebral subcortex8.15e-129
epithelium1.16e-11306
diencephalon1.55e-117
future diencephalon1.55e-117
cell layer1.92e-11309
temporal lobe2.81e-116
telencephalic nucleus8.86e-117
pons9.15e-113
limbic system1.35e-105
occipital lobe1.42e-105
parietal lobe1.60e-105
frontal cortex2.82e-103
medulla oblongata3.99e-103
myelencephalon3.99e-103
future myelencephalon3.99e-103
caudate-putamen5.12e-103
dorsal striatum5.12e-103
multi-tissue structure1.44e-08342
gland of diencephalon1.52e-084
neuroendocrine gland1.52e-084
pineal body3.28e-082
regional part of epithalamus3.28e-082
secretory circumventricular organ3.28e-082
circumventricular organ3.28e-082
epithalamus3.28e-082
regional part of diencephalon4.12e-084
Ammon's horn1.24e-072
lobe parts of cerebral cortex1.24e-072
hippocampal formation1.24e-072
limbic lobe1.24e-072
middle frontal gyrus1.29e-072
locus ceruleus1.46e-072
brainstem nucleus1.46e-072
hindbrain nucleus1.46e-072
middle temporal gyrus2.23e-072
caudate nucleus2.23e-072
future caudate nucleus2.23e-072


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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.10.0956087
MA0017.10.301634
MA0019.10.558663
MA0024.11.80828
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.13.04353
MA0031.11.69202
MA0038.10.514558
MA0040.11.8598
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.693769
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.11.99244
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0176541
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.11.0529
MA0145.10.046841
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.20.46405
MA0137.21.42372
MA0104.20.161609
MA0047.21.34084
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.11.57029
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.14518
MA0163.10.216998
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.104637
MA0102.21.41188
MA0258.10.180288
MA0259.10.624802
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
SUZ12#23512422.27368040491681.84044028319202e-050.000418492799338758



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:C961&oldid=2569472"