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Coexpression cluster:C1309: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,1.36287,0.267027,0.94331,0.553339,0.707204,1.85338,0.650887,0.391663,0.415981,2.06078,0.336106,0.236034,0.800617,0.436569,0.29639,0.576478,0.387783,1.21515,0.730467,0.202389,0.574247,0.396295,1.65122,0.530785,0.92701,0.816912,0.225641,0.35719,0.0334022,0.93226,0.585658,0.329602,0.248856,0.355745,0.513952,0.323162,2.68609,0.636689,1.18176,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,3.20696,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.181871,3.03424,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,0.234532,0.987239,0.776336,0.498077,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,1.56033,0.483695,1.74379,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,2.27213,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,2.00817,1.27379,2.40891,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,3.39081
|tfbs_overrepresentation_for_novel_motifs=1.12961,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,1.36287,0.267027,0.94331,0.553339,0.707204,1.85338,0.650887,0.391663,0.415981,2.06078,0.336106,0.236034,0.800617,0.436569,0.29639,0.576478,0.387783,1.21515,0.730467,0.202389,0.574247,0.396295,1.65122,0.530785,0.92701,0.816912,0.225641,0.35719,0.0334022,0.93226,0.585658,0.329602,0.248856,0.355745,0.513952,0.323162,2.68609,0.636689,1.18176,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,3.20696,0.500342,0.75612,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.181871,3.03424,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,0.234532,0.987239,0.776336,0.498077,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,1.56033,0.483695,1.74379,1.13818,0.978783,0.430775,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,2.27213,1.20639,0.692462,1.35529,0.999497,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,2.00817,1.27379,2.40891,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,3.39081
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.788761,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;0.906394,MA0050.1;0.545671,MA0051.1;1.58921,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;7.96111,MA0061.1;0.23892,MA0063.1;0,MA0066.1;3.92151,MA0067.1;1.35893,MA0068.1;1.09642,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.120085,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,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;1.02138,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.419295,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;1.84113,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;1.61362,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.093337,MA0147.1;0.87383,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.735746,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;1.88357,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;1.80563,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.0607789,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:50, 22 January 2013


Full id: C1309_putamen_parietal_caudate_temporal_duodenum_Neurons_occipital



Phase1 CAGE Peaks

Hg19::chr10:26505387..26505457,+p2@GAD2
Hg19::chr3:126113504..126113523,+p2@CCDC37
Hg19::chrX:82763261..82763262,+p4@POU3F4
Hg19::chrX:82763265..82763283,+p2@POU3F4
Hg19::chrX:82763292..82763317,+p1@POU3F4
Hg19::chrX:82763328..82763340,+p3@POU3F4


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:0006540glutamate decarboxylation to succinate0.003963990479922
GO:0004351glutamate decarboxylase activity0.003963990479922
GO:0006105succinate metabolic process0.003963990479922
GO:0006538glutamate catabolic process0.00445942365223706
GO:0043648dicarboxylic acid metabolic process0.0135880239617817
GO:0042136neurotransmitter biosynthetic process0.0135880239617817
GO:0006536glutamate metabolic process0.0135880239617817
GO:0009065glutamine family amino acid catabolic process0.0148610260391963
GO:0050877neurological system process0.0156469715618911
GO:0042133neurotransmitter metabolic process0.0172625772989556
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0172625772989556
GO:0003008system process0.0172625772989556
GO:0048839inner ear development0.0173713641720009
GO:0043583ear development0.017827455131619
GO:0016831carboxy-lyase activity0.0221807032804728
GO:0001505regulation of neurotransmitter levels0.0258326785076236
GO:0016830carbon-carbon lyase activity0.0258326785076236
GO:0009064glutamine family amino acid metabolic process0.0258326785076236
GO:0007423sensory organ development0.0258326785076236
GO:0009063amino acid catabolic process0.0258326785076236
GO:0009310amine catabolic process0.0259102216636778
GO:0044270nitrogen compound catabolic process0.0259102216636778
GO:0030170pyridoxal phosphate binding0.0301957734492803
GO:0050954sensory perception of mechanical stimulus0.0313347330006506
GO:0007605sensory perception of sound0.0313347330006506
GO:0032501multicellular organismal process0.049157105150703



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
oligodendrocyte9.86e-137
macroglial cell9.86e-137
astrocyte9.86e-137
oligodendrocyte precursor cell9.86e-137
neural cell8.17e-1225
neuronal stem cell3.50e-098
astrocyte of the cerebral cortex1.75e-083
astrocyte of the cerebellum3.60e-083
Uber Anatomy
Ontology termp-valuen
neural tube7.77e-12056
neural rod7.77e-12056
future spinal cord7.77e-12056
neural keel7.77e-12056
central nervous system6.52e-11681
regional part of nervous system6.74e-11353
regional part of brain6.74e-11353
nervous system4.66e-10389
brain6.61e-9668
future brain6.61e-9668
regional part of forebrain4.54e-8441
forebrain4.54e-8441
anterior neural tube4.54e-8441
future forebrain4.54e-8441
brain grey matter1.31e-8134
gray matter1.31e-8134
telencephalon2.05e-8134
neural plate6.97e-7882
presumptive neural plate6.97e-7882
cerebral hemisphere4.19e-7732
regional part of telencephalon9.43e-7732
neurectoderm1.18e-7386
ecto-epithelium4.50e-61104
cerebral cortex3.13e-5825
pallium3.13e-5825
pre-chordal neural plate2.16e-5361
regional part of cerebral cortex2.99e-5122
ectoderm-derived structure5.85e-49171
ectoderm5.85e-49171
presumptive ectoderm5.85e-49171
structure with developmental contribution from neural crest2.53e-47132
neocortex2.03e-4620
adult organism1.86e-43114
organ system subdivision9.31e-40223
posterior neural tube6.67e-3515
chordal neural plate6.67e-3515
segmental subdivision of hindbrain1.49e-2812
hindbrain1.49e-2812
presumptive hindbrain1.49e-2812
tube8.24e-27192
segmental subdivision of nervous system3.91e-2613
neural nucleus2.92e-249
nucleus of brain2.92e-249
basal ganglion3.53e-249
nuclear complex of neuraxis3.53e-249
aggregate regional part of brain3.53e-249
collection of basal ganglia3.53e-249
cerebral subcortex3.53e-249
regional part of metencephalon5.58e-229
metencephalon5.58e-229
future metencephalon5.58e-229
telencephalic nucleus1.19e-197
anatomical cluster2.66e-19373
anatomical conduit9.66e-19240
cerebellum2.64e-156
rhombic lip2.64e-156
gyrus5.84e-156
brainstem6.15e-156
organ part9.05e-15218
occipital lobe7.70e-145
parietal lobe8.80e-145
limbic system1.21e-135
temporal lobe2.43e-136
corpus striatum1.34e-124
striatum1.34e-124
ventral part of telencephalon1.34e-124
future corpus striatum1.34e-124
epithelium1.43e-12306
cell layer2.54e-12309
multi-tissue structure3.34e-11342
caudate-putamen6.22e-103
dorsal striatum6.22e-103
pons2.27e-083
medulla oblongata3.01e-083
myelencephalon3.01e-083
future myelencephalon3.01e-083
frontal cortex3.69e-083
organ3.94e-08503
spinal cord5.40e-083
dorsal region element5.40e-083
dorsum5.40e-083
caudate nucleus3.88e-072
future caudate nucleus3.88e-072
globus pallidus9.35e-072
pallidum9.35e-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
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
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
MA0048.10.906394
MA0050.10.545671
MA0051.11.58921
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.17.96111
MA0061.10.23892
MA0063.10
MA0066.13.92151
MA0067.11.35893
MA0068.11.09642
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.120085
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
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
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.093337
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.11.88357
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.273773
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.20.0607789
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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
SP1#666743.79892091876060.01052246616798510.0389396869151085



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:C1309&oldid=2569820"