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Coexpression cluster:C1303: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,1.11302,0.58616,1.01854,0.584466,0.662701,0.269608,0.267027,0.555913,0.553339,0.707204,0.635275,0.650887,1.01544,0.415981,2.06078,0.336106,0.236034,0.127969,0.436569,0.6169,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.316592,0.35388,1.43099,0.329602,0.69481,0.355745,0.513952,0.0979105,1.01199,0.154075,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,1.43182,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,1.35522,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,1.17153,0.206105,0.192925,0.84426,0.913168,2.08653,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,18.5831,1.02636,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,2.70383,0.864356,0.234532,0.987239,0.776336,0.962826,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,5.60657,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.639143,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,4.22505,1.15112,1.27379,1.06043,2.10728,0.457485,0.83286,0.683502,0.79772,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,1.11302,0.58616,1.01854,0.584466,0.662701,0.269608,0.267027,0.555913,0.553339,0.707204,0.635275,0.650887,1.01544,0.415981,2.06078,0.336106,0.236034,0.127969,0.436569,0.6169,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.316592,0.35388,1.43099,0.329602,0.69481,0.355745,0.513952,0.0979105,1.01199,0.154075,0.468392,0.66382,0.542147,0.0909286,1.02586,0.745008,0.675919,1.43182,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,1.35522,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,1.17153,0.206105,0.192925,0.84426,0.913168,2.08653,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,18.5831,1.02636,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,2.70383,0.864356,0.234532,0.987239,0.776336,0.962826,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,1.57878,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,5.60657,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.639143,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,4.22505,1.15112,1.27379,1.06043,2.10728,0.457485,0.83286,0.683502,0.79772,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;2.36092,MA0014.1;0.108006,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;2.08744,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.808182,MA0056.1;0,MA0057.1;0.882847,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;11.7007,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.660742,MA0089.1;0,MA0090.1;1.22966,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;1.12205,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;1.15452,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.0270301,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.166826,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:50, 22 January 2013


Full id: C1303_hippocampus_pituitary_insula_medulla_medial_occipital_paracentral



Phase1 CAGE Peaks

Hg19::chr10:125425217..125425232,+p@chr10:125425217..125425232
+
Hg19::chr11:81359062..81359117,-p@chr11:81359062..81359117
-
Hg19::chr11:81359124..81359143,-p@chr11:81359124..81359143
-
Hg19::chr11:81359178..81359208,-p@chr11:81359178..81359208
-
Hg19::chr6:152793728..152793766,-p14@SYNE1
Hg19::chrX:151619719..151619724,-p3@GABRA3


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:0045211postsynaptic membrane0.000948648538551125
GO:0044456synapse part0.000948648538551125
GO:0005521lamin binding0.00875643846671322
GO:0008503benzodiazepine receptor activity0.00875643846671322
GO:0007030Golgi organization and biogenesis0.014008857951139
GO:0007214gamma-aminobutyric acid signaling pathway0.0216765454530563
GO:0006997nuclear organization and biogenesis0.0235034451487031
GO:0004890GABA-A receptor activity0.0235034451487031
GO:0042692muscle cell differentiation0.0235034451487031
GO:0016917GABA receptor activity0.0235034451487031
GO:0043168anion binding0.0249988776174169
GO:0031404chloride ion binding0.0249988776174169
GO:0005254chloride channel activity0.0310576757163792
GO:0006821chloride transport0.0310576757163792
GO:0005253anion channel activity0.0333121960667309
GO:0005230extracellular ligand-gated ion channel activity0.0389860458602887
GO:0030594neurotransmitter receptor activity0.0389860458602887
GO:0042165neurotransmitter binding0.0389860458602887
GO:0031965nuclear membrane0.0389860458602887
GO:0015276ligand-gated ion channel activity0.0389860458602887
GO:0022834ligand-gated channel activity0.0389860458602887
GO:0005635nuclear envelope0.0440018987458718
GO:0008509anion transmembrane transporter activity0.0453330200615595



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
neural tube1.78e-10056
neural rod1.78e-10056
future spinal cord1.78e-10056
neural keel1.78e-10056
regional part of nervous system1.16e-9153
regional part of brain1.16e-9153
central nervous system8.06e-9181
regional part of forebrain8.43e-8641
forebrain8.43e-8641
anterior neural tube8.43e-8641
future forebrain8.43e-8641
brain6.90e-8468
future brain6.90e-8468
nervous system8.51e-8189
telencephalon1.60e-8034
brain grey matter1.75e-8034
gray matter1.75e-8034
cerebral hemisphere4.98e-7532
regional part of telencephalon2.55e-7432
neural plate7.51e-6982
presumptive neural plate7.51e-6982
regional part of cerebral cortex4.96e-6822
neurectoderm3.49e-6586
neocortex3.81e-6120
cerebral cortex1.80e-5925
pallium1.80e-5925
pre-chordal neural plate1.47e-5861
ecto-epithelium9.62e-55104
adult organism1.39e-54114
structure with developmental contribution from neural crest4.58e-43132
ectoderm-derived structure8.62e-41171
ectoderm8.62e-41171
presumptive ectoderm8.62e-41171
organ system subdivision6.77e-33223
tube9.51e-25192
basal ganglion5.37e-229
nuclear complex of neuraxis5.37e-229
aggregate regional part of brain5.37e-229
collection of basal ganglia5.37e-229
cerebral subcortex5.37e-229
neural nucleus7.56e-229
nucleus of brain7.56e-229
gyrus3.06e-216
brainstem8.55e-206
anatomical conduit1.06e-18240
limbic system6.83e-185
parietal lobe1.89e-175
temporal lobe4.10e-176
occipital lobe6.54e-175
anatomical cluster9.23e-17373
posterior neural tube2.16e-1615
chordal neural plate2.16e-1615
telencephalic nucleus5.87e-167
epithelium5.26e-14306
cell layer9.23e-14309
frontal cortex1.95e-113
organ part4.45e-11218
pons8.65e-113
medulla oblongata9.88e-113
myelencephalon9.88e-113
future myelencephalon9.88e-113
multi-tissue structure1.33e-10342
spinal cord2.04e-103
dorsal region element2.04e-103
dorsum2.04e-103
organ7.69e-10503
segmental subdivision of hindbrain1.51e-0912
hindbrain1.51e-0912
presumptive hindbrain1.51e-0912
segmental subdivision of nervous system9.29e-0913
Ammon's horn1.73e-082
lobe parts of cerebral cortex1.73e-082
hippocampal formation1.73e-082
limbic lobe1.73e-082
pituitary gland2.00e-082
middle frontal gyrus3.50e-082
middle temporal gyrus4.30e-082
corpus striatum5.21e-084
striatum5.21e-084
ventral part of telencephalon5.21e-084
future corpus striatum5.21e-084
diencephalon5.70e-087
future diencephalon5.70e-087
amygdala6.50e-082
locus ceruleus9.75e-082
brainstem nucleus9.75e-082
hindbrain nucleus9.75e-082
embryo1.20e-07592
germ layer1.64e-07560
germ layer / neural crest1.64e-07560
embryonic tissue1.64e-07560
presumptive structure1.64e-07560
germ layer / neural crest derived structure1.64e-07560
epiblast (generic)1.64e-07560
developing anatomical structure2.07e-07581
embryonic structure2.29e-07564
globus pallidus2.54e-072
pallidum2.54e-072
dorsal plus ventral thalamus3.19e-072
thalamic complex3.19e-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)
MA0003.10.00461978
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.12.36092
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.08744
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.111.7007
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.11.12205
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.11.15452
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.166826
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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:C1303&oldid=2569814"