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Coexpression cluster:C841: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0405018798333213,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.299757310563537,0.105030956603628,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.147159551208692,0.263059703982291,0,0,0,0,0,0,0,0,0,0,0.137741066253898,0.187944965404633,0.402401944384513,0.520456669291998,0.931212945965072,0.0861409897892114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.079294329153405,0,0.25915225909417,0,0,0,0,0,0.0579836861320005,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.080977547656084,0,0,0.119438670232611,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.204234048342335,0.149439634110414,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.254120022070344,0.148790834525069,0,0,0,0,0,0.125083138191402,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.198781287708291,0.219031910159205,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.275557388108753,0.356775332814486,0.273310730353101,0.196841684047034,0.190522922498466,0.103797139000423,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.308727619171225,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0418542907017061,0,0,0,0,0,0,0,0.168200649575827,0.483457425382718,0.291769023891927,0.204736616091788,0.171103451149497,0.116308042208012,0.216404126670406,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.187605506286389,0,0.284954262086088,0.139576084081964,0.320966228024776,0,0,0,0,0,0,0,0,0,0,0,0.177919139297545,0.19276857886417,0,0,0,0.22805966801922,0,0,0,0,0.0149913341442922,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.197763394667016,0,0.15309981666883,0,0,0,0,0,0,0,0,0,0.205616485139479,0,0.0806172781120618,0.157260487458867,0,0,0,0,0,0,0,0,0,0,0,0,0,0.262253936867136,0.18103280933514,0,0,0.0135909688377214,0,0,0,0.039973403565921,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C841_cerebellum_occipital_medial_parietal_middle_caudate_globus|gostat_on_coexpression_clusters=GO:0018318!protein amino acid palmitoylation!0.00123631225715295!79929$GO:0018009!N-terminal peptidyl-L-cysteine N-palmitoylation!0.00123631225715295!79929$GO:0006500!N-terminal protein palmitoylation!0.00123631225715295!79929$GO:0018198!peptidyl-cysteine modification!0.00123631225715295!79929$GO:0018345!protein palmitoylation!0.00395602453569053!79929$GO:0006498!N-terminal protein lipidation!0.00576894769571694!79929$GO:0005801!cis-Golgi network!0.00847619722105734!79929$GO:0018409!peptide or protein amino-terminal blocking!0.0086525299109976!79929$GO:0031365!N-terminal protein amino acid modification!0.00874645367489492!79929$GO:0007026!negative regulation of microtubule depolymerization!0.00874645367489492!79929$GO:0031114!regulation of microtubule depolymerization!0.00874645367489492!79929$GO:0007019!microtubule depolymerization!0.00874645367489492!79929$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.00874645367489492!79929$GO:0031110!regulation of microtubule polymerization or depolymerization!0.00988598530458499!79929$GO:0043543!protein amino acid acylation!0.00988598530458499!79929$GO:0031109!microtubule polymerization or depolymerization!0.00988598530458499!79929$GO:0006996!organelle organization and biogenesis!0.00996380673908192!124359;79929$GO:0051261!protein depolymerization!0.0123532964165906!79929$GO:0008017!microtubule binding!0.0123532964165906!79929$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0123532964165906!79929$GO:0006497!protein amino acid lipidation!0.0123532964165906!79929$GO:0042158!lipoprotein biosynthetic process!0.0123532964165906!79929$GO:0015631!tubulin binding!0.0142033612291807!79929$GO:0005798!Golgi-associated vesicle!0.0142033612291807!79929$GO:0042157!lipoprotein metabolic process!0.0165957380836218!79929$GO:0051128!regulation of cellular component organization and biogenesis!0.0183402218492073!79929$GO:0000226!microtubule cytoskeleton organization and biogenesis!0.0183402218492073!79929$GO:0051248!negative regulation of protein metabolic process!0.0183402218492073!79929$GO:0003682!chromatin binding!0.0199106091636198!124359$GO:0018193!peptidyl-amino acid modification!0.0199106091636198!79929$GO:0005516!calmodulin binding!0.0224465584136513!79929$GO:0016043!cellular component organization and biogenesis!0.0244185682156788!124359;79929$GO:0044446!intracellular organelle part!0.0365061351107608!124359;79929$GO:0044422!organelle part!0.0365061351107608!124359;79929$GO:0006333!chromatin assembly or disassembly!0.0384185189393315!124359$GO:0007017!microtubule-based process!0.0428336985479389!79929$GO:0000785!chromatin!0.0428336985479389!124359$GO:0016023!cytoplasmic membrane-bound vesicle!0.0444034554120826!79929$GO:0031988!membrane-bound vesicle!0.0444034554120826!79929$GO:0044431!Golgi apparatus part!0.0484884833151138!79929$GO:0051246!regulation of protein metabolic process!0.0484884833151138!79929$GO:0031410!cytoplasmic 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126492,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;0.241637,MA0103.1;0.228129,MA0105.1;0.189717,MA0106.1;0.516528,MA0107.1;0.179177,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;0.532314,MA0114.1;0.51954,MA0115.1;2.42332,MA0116.1;0.182037,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.353333,MA0140.1;0.437738,MA0141.1;1.43869,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;11.622,MA0145.1;0.0359093,MA0146.1;0.0551603,MA0147.1;0.184931,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;0.0721026,MA0138.2;0.569505,MA0002.2;0.129981,MA0137.2;13.8232,MA0104.2;0.138396,MA0047.2;0.504873,MA0112.2;0.0329985,MA0065.2;0.615279,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.414714,MA0155.1;0.12484,MA0156.1;2.0352,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.185458,MA0160.1;0.417847,MA0161.1;0,MA0162.1;0.403951,MA0163.1;0.162989,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;0.227142,MA0102.2;1.36707,MA0258.1;0.155735,MA0259.1;0.560522,MA0442.1;0}}
|full_id=C841_cerebellum_occipital_medial_parietal_middle_caudate_globus
|id=C841
}}

Latest revision as of 11:32, 17 September 2013


Full id: C841_cerebellum_occipital_medial_parietal_middle_caudate_globus



Phase1 CAGE Peaks

Hg19::chr16:80838247..80838258,-p8@CDYL2
Hg19::chr19:49149232..49149245,+p@chr19:49149232..49149245
+
Hg19::chr19:6494729..6494749,+p@chr19:6494729..6494749
+
Hg19::chr20:10288445..10288449,+p@chr20:10288445..10288449
+
Hg19::chr3:120776122..120776137,+p@chr3:120776122..120776137
+
Hg19::chr3:183543817..183543832,-p5@MAP6D1
Hg19::chrX:139866190..139866197,-p5@CDR1
Hg19::chrX:139866214..139866221,+p@chrX:139866214..139866221
+
Hg19::chrX:139866339..139866349,+p@chrX:139866339..139866349
+
Hg19::chrX:153094936..153094950,-p@chrX:153094936..153094950
-


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:0018318protein amino acid palmitoylation0.00123631225715295
GO:0018009N-terminal peptidyl-L-cysteine N-palmitoylation0.00123631225715295
GO:0006500N-terminal protein palmitoylation0.00123631225715295
GO:0018198peptidyl-cysteine modification0.00123631225715295
GO:0018345protein palmitoylation0.00395602453569053
GO:0006498N-terminal protein lipidation0.00576894769571694
GO:0005801cis-Golgi network0.00847619722105734
GO:0018409peptide or protein amino-terminal blocking0.0086525299109976
GO:0031365N-terminal protein amino acid modification0.00874645367489492
GO:0007026negative regulation of microtubule depolymerization0.00874645367489492
GO:0031114regulation of microtubule depolymerization0.00874645367489492
GO:0007019microtubule depolymerization0.00874645367489492
GO:0031111negative regulation of microtubule polymerization or depolymerization0.00874645367489492
GO:0031110regulation of microtubule polymerization or depolymerization0.00988598530458499
GO:0043543protein amino acid acylation0.00988598530458499
GO:0031109microtubule polymerization or depolymerization0.00988598530458499
GO:0006996organelle organization and biogenesis0.00996380673908192
GO:0051261protein depolymerization0.0123532964165906
GO:0008017microtubule binding0.0123532964165906
GO:0051129negative regulation of cellular component organization and biogenesis0.0123532964165906
GO:0006497protein amino acid lipidation0.0123532964165906
GO:0042158lipoprotein biosynthetic process0.0123532964165906
GO:0015631tubulin binding0.0142033612291807
GO:0005798Golgi-associated vesicle0.0142033612291807
GO:0042157lipoprotein metabolic process0.0165957380836218
GO:0051128regulation of cellular component organization and biogenesis0.0183402218492073
GO:0000226microtubule cytoskeleton organization and biogenesis0.0183402218492073
GO:0051248negative regulation of protein metabolic process0.0183402218492073
GO:0003682chromatin binding0.0199106091636198
GO:0018193peptidyl-amino acid modification0.0199106091636198
GO:0005516calmodulin binding0.0224465584136513
GO:0016043cellular component organization and biogenesis0.0244185682156788
GO:0044446intracellular organelle part0.0365061351107608
GO:0044422organelle part0.0365061351107608
GO:0006333chromatin assembly or disassembly0.0384185189393315
GO:0007017microtubule-based process0.0428336985479389
GO:0000785chromatin0.0428336985479389
GO:0016023cytoplasmic membrane-bound vesicle0.0444034554120826
GO:0031988membrane-bound vesicle0.0444034554120826
GO:0044431Golgi apparatus part0.0484884833151138
GO:0051246regulation of protein metabolic process0.0484884833151138
GO:0031410cytoplasmic vesicle0.0484884833151138
GO:0031982vesicle0.0484884833151138
GO:0009892negative regulation of metabolic process0.0484884833151138
GO:0006325establishment and/or maintenance of chromatin architecture0.0484884833151138
GO:0006323DNA packaging0.0484884833151138
GO:0044427chromosomal part0.0484884833151138



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 tube4.66e-11956
neural rod4.66e-11956
future spinal cord4.66e-11956
neural keel4.66e-11956
regional part of nervous system1.82e-11453
regional part of brain1.82e-11453
brain3.45e-9568
future brain3.45e-9568
central nervous system1.13e-9081
brain grey matter1.02e-8934
gray matter1.02e-8934
regional part of forebrain1.17e-8941
forebrain1.17e-8941
anterior neural tube1.17e-8941
future forebrain1.17e-8941
telencephalon3.36e-8934
regional part of telencephalon1.27e-8232
cerebral hemisphere1.70e-8232
neural plate2.30e-8282
presumptive neural plate2.30e-8282
neurectoderm9.10e-8286
nervous system8.39e-8189
regional part of cerebral cortex2.39e-6722
ecto-epithelium5.37e-63104
pre-chordal neural plate1.06e-6161
neocortex1.87e-6020
cerebral cortex6.10e-5925
pallium6.10e-5925
adult organism5.43e-57114
structure with developmental contribution from neural crest1.48e-52132
ectoderm-derived structure1.15e-41171
ectoderm1.15e-41171
presumptive ectoderm1.15e-41171
neural nucleus2.71e-329
nucleus of brain2.71e-329
basal ganglion4.06e-329
nuclear complex of neuraxis4.06e-329
aggregate regional part of brain4.06e-329
collection of basal ganglia4.06e-329
cerebral subcortex4.06e-329
organ system subdivision3.75e-31223
posterior neural tube1.10e-2815
chordal neural plate1.10e-2815
tube4.19e-28192
telencephalic nucleus2.61e-257
segmental subdivision of hindbrain1.58e-2412
hindbrain1.58e-2412
presumptive hindbrain1.58e-2412
gyrus3.26e-236
segmental subdivision of nervous system1.66e-2213
brainstem6.29e-226
anatomical conduit1.68e-20240
occipital lobe4.26e-195
temporal lobe8.40e-196
limbic system1.30e-185
organ part3.72e-18218
epithelium8.64e-17306
cell layer1.58e-16309
anatomical cluster2.54e-16373
regional part of metencephalon2.31e-159
metencephalon2.31e-159
future metencephalon2.31e-159
corpus striatum4.06e-154
striatum4.06e-154
ventral part of telencephalon4.06e-154
future corpus striatum4.06e-154
multi-tissue structure7.12e-14342
parietal lobe1.38e-125
frontal cortex3.76e-123
pons4.89e-123
caudate-putamen7.94e-123
dorsal striatum7.94e-123
medulla oblongata1.24e-113
myelencephalon1.24e-113
future myelencephalon1.24e-113
organ2.96e-09503
middle temporal gyrus3.44e-092
middle frontal gyrus5.30e-092
locus ceruleus1.06e-082
brainstem nucleus1.06e-082
hindbrain nucleus1.06e-082
dorsal plus ventral thalamus1.19e-082
thalamic complex1.19e-082
amygdala1.61e-082
Ammon's horn1.67e-082
lobe parts of cerebral cortex1.67e-082
hippocampal formation1.67e-082
limbic lobe1.67e-082
globus pallidus2.01e-082
pallidum2.01e-082
caudate nucleus2.92e-082
future caudate nucleus2.92e-082
germ layer7.99e-08560
germ layer / neural crest7.99e-08560
embryonic tissue7.99e-08560
presumptive structure7.99e-08560
germ layer / neural crest derived structure7.99e-08560
epiblast (generic)7.99e-08560
embryonic structure1.09e-07564
embryo2.01e-07592


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)
MA0003.10.456919
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.15363
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.11.02846
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.0580131
MA0058.10.796055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.0824235
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.189717
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.51954
MA0115.12.42332
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.353333
MA0140.10.437738
MA0141.11.43869
MA0142.10.638837
MA0143.10.532484
MA0144.111.622
MA0145.10.0359093
MA0146.10.0551603
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0721026
MA0138.20.569505
MA0002.20.129981
MA0137.213.8232
MA0104.20.138396
MA0047.20.504873
MA0112.20.0329985
MA0065.20.615279
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.12484
MA0156.12.0352
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.403951
MA0163.10.162989
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.227142
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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.

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