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Coexpression cluster:C561: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.928065,0.838608,0.907146,0.258928,0.125522,0.25764,0.854181,0.0594415,0.463955,1.21535,0.660906,0.355038,1.42611,0.309388,0.124662,0.139688,0.511522,0.0927064,1.06622,0.306606,0.152859,0.179594,0.251588,0.12232,1.03735,0.374311,0.309883,0.249905,0.400769,0.509928,0.217756,0.544857,0.552347,0.363901,0.694555,3.05677,0.33558,0.258546,0.0891992,3.31089,0.338389,1.12058,0.0333136,0.123709,0.321633,0.173971,0.319738,0.226038,0.18831,0.798822,0.386472,0.878028,0.625622,0.615394,0.758742,0.838357,0.130259,0.2852,0.274137,1.41706,0.582323,0.321692,0.212582,0.48664,0.336598,0.456015,0.843028,1.20113,0.535417,1.04233,0.570382,0.0621482,0.918604,0.756844,1.39608,0.318394,1.6609,1.18857,0.532468,0.18023,0.0470011,1.21884,0.336303,0.0607686,0.70821,2.84424,0.149619,1.15199,0.408949,1.29895,0.932961,0.68283,0.560183,0.270867,0.791919,0.0858933,0.684177,0.599297,1.06191,0.437614,0.301599,0.555021,0.594155,0.514828,0.445845,0.652834,0.500571,0.826592,0.542462,1.78316,2.14812,0.591605,0.455599,0.677747,0.886618,0.101627,3.64989,0.619973,0.453946,0.578957,0.748992,0.406842,0.255485,0.345739,0.993708,1.19002,0.842452,0.564749,0.78949,0.291925,0.683478,0.219902,0.803201,0.342946,0.945426,0.757411,0.21329,0.698255,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.76278,0.432737,1.59165,0.203207,0.562706,0.169169,1.44662,0.683836,3.42069,0.321292,1.07219,0.394947,0.116843,0.184652,0.164414,0.867287,0.66649,0.531753,0.166635,0.46162,0.891749,0.0708512,0.317742,0.939778
|tfbs_overrepresentation_for_novel_motifs=0.928065,0.838608,0.907146,0.258928,0.125522,0.25764,0.854181,0.0594415,0.463955,1.21535,0.660906,0.355038,1.42611,0.309388,0.124662,0.139688,0.511522,0.0927064,1.06622,0.306606,0.152859,0.179594,0.251588,0.12232,1.03735,0.374311,0.309883,0.249905,0.400769,0.509928,0.217756,0.544857,0.552347,0.363901,0.694555,3.05677,0.33558,0.258546,0.0891992,3.31089,0.338389,1.12058,0.0333136,0.123709,0.321633,0.173971,0.319738,0.226038,0.18831,0.798822,0.386472,0.878028,0.625622,0.615394,0.758742,0.838357,0.130259,0.2852,0.274137,1.41706,0.582323,0.321692,0.212582,0.48664,0.336598,0.456015,0.843028,1.20113,0.535417,1.04233,0.570382,0.0621482,0.918604,0.756844,1.39608,0.318394,1.6609,1.18857,0.532468,0.18023,0.0470011,1.21884,0.336303,0.0607686,0.70821,2.84424,0.149619,1.15199,0.408949,1.29895,0.932961,0.68283,0.560183,0.270867,0.791919,0.0858933,0.684177,0.599297,1.06191,0.437614,0.301599,0.555021,0.594155,0.514828,0.445845,0.652834,0.500571,0.826592,0.542462,1.78316,2.14812,0.591605,0.455599,0.677747,0.886618,0.101627,3.64989,0.619973,0.453946,0.578957,0.748992,0.406842,0.255485,0.345739,0.993708,1.19002,0.842452,0.564749,0.78949,0.291925,0.683478,0.219902,0.803201,0.342946,0.945426,0.757411,0.21329,0.698255,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.76278,0.432737,1.59165,0.203207,0.562706,0.169169,1.44662,0.683836,3.42069,0.321292,1.07219,0.394947,0.116843,0.184652,0.164414,0.867287,0.66649,0.531753,0.166635,0.46162,0.891749,0.0708512,0.317742,0.939778
|tfbs_overrepresentation_jaspar=MA0003.1;3.09978,MA0004.1;0.670242,MA0006.1;0.124371,MA0007.1;0.223897,MA0009.1;0.644692,MA0014.1;4.30017,MA0017.1;0.150184,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.227947,MA0043.1;0.644989,MA0046.1;0.634468,MA0048.1;0.643709,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;0.499384,MA0056.1;0,MA0057.1;0.91959,MA0058.1;0.968374,MA0059.1;0.499176,MA0060.1;0.464905,MA0061.1;1.08093,MA0063.1;0,MA0066.1;0.321498,MA0067.1;0.948938,MA0068.1;1.2688,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;0.616162,MA0073.1;0.589869,MA0074.1;0.316991,MA0076.1;0.178863,MA0077.1;0.608956,MA0078.1;0.402443,MA0081.1;0.499456,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.369952,MA0089.1;0,MA0090.1;0.189305,MA0091.1;0.240316,MA0092.1;0.607109,MA0093.1;0.793328,MA0095.1;0,MA0098.1;0,MA0100.1;0.332778,MA0101.1;0.128426,MA0103.1;0.377626,MA0105.1;1.1728,MA0106.1;0.355999,MA0107.1;0.285979,MA0108.2;1.23385,MA0109.1;0,MA0111.1;0.199239,MA0113.1;0.968027,MA0114.1;0.0814649,MA0115.1;0.874839,MA0116.1;0.0861811,MA0117.1;0.680135,MA0119.1;0.155538,MA0122.1;0.70466,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.327047,MA0139.1;0.652922,MA0140.1;0.286995,MA0141.1;0.165463,MA0142.1;0.4668,MA0143.1;0.370225,MA0144.1;0.25687,MA0145.1;0.113672,MA0146.1;0.250667,MA0147.1;0.296651,MA0148.1;0.257816,MA0149.1;0.279141,MA0062.2;0.0439512,MA0035.2;0.286421,MA0039.2;2.70787,MA0138.2;0.403517,MA0002.2;0.196222,MA0137.2;0.138998,MA0104.2;0.462925,MA0047.2;0.345656,MA0112.2;0.390337,MA0065.2;0.955706,MA0150.1;0.5439,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.321153,MA0155.1;1.88309,MA0156.1;0.140505,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.619098,MA0160.1;0.26995,MA0161.1;0,MA0162.1;2.47439,MA0163.1;3.11055,MA0164.1;0.380804,MA0080.2;0.126365,MA0018.2;0.939567,MA0099.2;0.292649,MA0079.2;18.6848,MA0102.2;1.16862,MA0258.1;0.0689091,MA0259.1;0.309645,MA0442.1;0
}}
}}

Revision as of 19:16, 22 January 2013


Full id: C561_brain_Neural_spinal_Neurons_parietal_temporal_occipital



Phase1 CAGE Peaks

Hg19::chr11:65816664..65816675,-p2@GAL3ST3
Hg19::chr13:36705425..36705445,-p5@DCLK1
Hg19::chr13:53422767..53422780,-p1@PCDH8
Hg19::chr19:19322758..19322773,+p1@NCAN
Hg19::chr19:19322805..19322812,+p2@NCAN
Hg19::chr1:156391550..156391569,-p2@C1orf61
Hg19::chr1:156399211..156399225,-p1@C1orf61
Hg19::chr1:156400037..156400063,-p@chr1:156400037..156400063
-
Hg19::chr22:42372970..42372971,+p5@SEPT3
Hg19::chr2:26395939..26396015,+p2@FAM59B
Hg19::chr3:26664252..26664268,+p5@LRRC3B
Hg19::chr3:65387362..65387385,-p14@MAGI1
Hg19::chr4:150999554..150999573,+p6@DCLK2
Hg19::chr5:140787600..140787637,+p2@PCDHGB6
Hg19::chr5:87968909..87968913,-p2@LINC00461
Hg19::chr5:87969130..87969153,-p1@LINC00461


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:0022610biological adhesion0.00364590195774595
GO:0007155cell adhesion0.00364590195774595
GO:0016337cell-cell adhesion0.00364590195774595
GO:0050698proteoglycan sulfotransferase activity0.0170795551236903
GO:0030309poly-N-acetyllactosamine metabolic process0.0170795551236903
GO:0050694galactose 3-O-sulfotransferase activity0.0170795551236903
GO:0001733galactosylceramide sulfotransferase activity0.0170795551236903
GO:0017076purine nucleotide binding0.0170795551236903
GO:0007156homophilic cell adhesion0.0170795551236903
GO:00506563'-phosphoadenosine 5'-phosphosulfate binding0.0170795551236903
GO:0007158neuron adhesion0.0217324972662446
GO:0000166nucleotide binding0.0271439940753673
GO:0030554adenyl nucleotide binding0.0468748694812944
GO:0030166proteoglycan biosynthetic process0.0468748694812944
GO:0005509calcium ion binding0.0468748694812944
GO:0009311oligosaccharide metabolic process0.0468748694812944



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 cell1.58e-158
neural cell1.02e-1225
neuron1.80e-116
neuroblast1.80e-116
electrically signaling cell1.80e-116
neurectodermal cell3.70e-0759
oligodendrocyte9.30e-077
macroglial cell9.30e-077
astrocyte9.30e-077
oligodendrocyte precursor cell9.30e-077
Uber Anatomy
Ontology termp-valuen
central nervous system3.98e-9681
nervous system1.86e-9589
neural tube2.70e-8956
neural rod2.70e-8956
future spinal cord2.70e-8956
neural keel2.70e-8956
regional part of nervous system1.13e-8353
regional part of brain1.13e-8353
brain1.28e-7268
future brain1.28e-7268
regional part of forebrain1.20e-6641
forebrain1.20e-6641
anterior neural tube1.20e-6641
future forebrain1.20e-6641
neurectoderm2.08e-6686
neural plate3.56e-6382
presumptive neural plate3.56e-6382
telencephalon3.07e-6234
brain grey matter5.98e-6234
gray matter5.98e-6234
cerebral hemisphere7.80e-5932
regional part of telencephalon1.84e-5832
ectoderm-derived structure1.50e-49171
ectoderm1.50e-49171
presumptive ectoderm1.50e-49171
ecto-epithelium3.88e-48104
pre-chordal neural plate5.32e-4861
adult organism3.31e-46114
cerebral cortex7.61e-4625
pallium7.61e-4625
regional part of cerebral cortex1.01e-4022
organ system subdivision8.07e-38223
structure with developmental contribution from neural crest2.42e-37132
neocortex9.28e-3720
posterior neural tube1.55e-2215
chordal neural plate1.55e-2215
segmental subdivision of nervous system7.12e-1913
anatomical cluster3.23e-18373
basal ganglion1.76e-179
nuclear complex of neuraxis1.76e-179
aggregate regional part of brain1.76e-179
collection of basal ganglia1.76e-179
cerebral subcortex1.76e-179
segmental subdivision of hindbrain2.10e-1712
hindbrain2.10e-1712
presumptive hindbrain2.10e-1712
neural nucleus3.62e-179
nucleus of brain3.62e-179
tube1.42e-16192
telencephalic nucleus7.61e-147
regional part of metencephalon1.14e-129
metencephalon1.14e-129
future metencephalon1.14e-129
gyrus1.29e-126
anatomical conduit1.57e-11240
brainstem2.25e-116
limbic system3.22e-115
parietal lobe4.94e-115
temporal lobe6.09e-116
occipital lobe8.00e-115
organ part1.69e-10218
embryo2.63e-10592
corpus striatum4.81e-094
striatum4.81e-094
ventral part of telencephalon4.81e-094
future corpus striatum4.81e-094
developing anatomical structure2.84e-08581
embryonic structure2.96e-08564
germ layer5.62e-08560
germ layer / neural crest5.62e-08560
embryonic tissue5.62e-08560
presumptive structure5.62e-08560
germ layer / neural crest derived structure5.62e-08560
epiblast (generic)5.62e-08560
regional part of diencephalon7.09e-084
cerebellum7.14e-086
rhombic lip7.14e-086
multi-tissue structure1.11e-07342
epithelium1.71e-07306
cell layer2.75e-07309
frontal cortex4.59e-073
caudate-putamen4.78e-073
dorsal striatum4.78e-073
multi-cellular organism6.51e-07656
spinal cord7.70e-073
dorsal region element7.70e-073
dorsum7.70e-073
diencephalon9.79e-077
future diencephalon9.79e-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)
MA0003.13.09978
MA0004.10.670242
MA0006.10.124371
MA0007.10.223897
MA0009.10.644692
MA0014.14.30017
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.10.643709
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.499384
MA0056.10
MA0057.10.91959
MA0058.10.968374
MA0059.10.499176
MA0060.10.464905
MA0061.11.08093
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.11.2688
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.589869
MA0074.10.316991
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.369952
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.607109
MA0093.10.793328
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.128426
MA0103.10.377626
MA0105.11.1728
MA0106.10.355999
MA0107.10.285979
MA0108.21.23385
MA0109.10
MA0111.10.199239
MA0113.10.968027
MA0114.10.0814649
MA0115.10.874839
MA0116.10.0861811
MA0117.10.680135
MA0119.10.155538
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.652922
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.25687
MA0145.10.113672
MA0146.10.250667
MA0147.10.296651
MA0148.10.257816
MA0149.10.279141
MA0062.20.0439512
MA0035.20.286421
MA0039.22.70787
MA0138.20.403517
MA0002.20.196222
MA0137.20.138998
MA0104.20.462925
MA0047.20.345656
MA0112.20.390337
MA0065.20.955706
MA0150.10.5439
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.321153
MA0155.11.88309
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.619098
MA0160.10.26995
MA0161.10
MA0162.12.47439
MA0163.13.11055
MA0164.10.380804
MA0080.20.126365
MA0018.20.939567
MA0099.20.292649
MA0079.218.6848
MA0102.21.16862
MA0258.10.0689091
MA0259.10.309645
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#2351239.39670892082430.003659155081411430.0184760441668695



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:C561&oldid=2569072"