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Coexpression cluster:C1482: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.333388,1.11302,0.58616,0.393082,0.584466,1.59238,0.269608,0.267027,0.94331,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,2.54699,0.436569,0.0880431,1.41165,0.387783,1.21515,0.730467,0.202389,1.40695,1.02557,0.186644,0.530785,0.92701,0.816912,0.225641,1.67655,0.134746,0.35388,0.585658,0.329602,0.69481,0.355745,2.20706,0.323162,0.390088,1.41477,0.468392,0.66382,1.33909,0.0909286,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,1.41895,1.15727,1.17153,3.28695,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,8.58788,1.87735,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,2.321,0.877269,0.647343,1.21459,3.59277,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,2.24955,1.31236,1.9262,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,2.18236,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,1.9604,4.24288,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,4.05264,1.27379,1.06043,0.912368,4.07199,0.83286,0.683502,0.29379,0.661335,0.792495
|tfbs_overrepresentation_jaspar=MA0003.1;4.08206,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;1.149,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;3.56533,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;2.26581,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;1.15845,MA0060.1;2.90543,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;10.33,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;0.490736,MA0091.1;0.561458,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.02896,MA0103.1;0.381434,MA0105.1;1.34409,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;0.440684,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;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;1.16614,MA0146.1;2.38407,MA0147.1;1.57246,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;3.75773,MA0138.2;3.01409,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;2.08061,MA0047.2;0.695777,MA0112.2;0.332548,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;2.1986,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;2.40092,MA0163.1;0.508943,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;5.61874,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1482_caudate_anaplastic_putamen_thalamus_small_diencephalon_nucleus



Phase1 CAGE Peaks

Hg19::chr20:60795296..60795309,-p2@HRH3
Hg19::chr20:60795316..60795323,-p3@HRH3
Hg19::chr20:60795326..60795340,-p1@HRH3
Hg19::chr2:242089628..242089643,-p5@PASK
Hg19::chr3:58810185..58810229,+p1@ENST00000463703
p1@ENST00000482372
p1@uc003dku.1
Hg19::chr4:72102152..72102166,+p16@SLC4A4


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:0008510sodium:bicarbonate symporter activity0.0323188318986822
GO:0004969histamine receptor activity0.0475105037576734
GO:0015106bicarbonate transmembrane transporter activity0.0475105037576734
GO:0005452inorganic anion exchanger activity0.0475105037576734
GO:0015380anion exchanger activity0.0475105037576734
GO:0015301anion:anion antiporter activity0.0475105037576734
GO:0015108chloride transmembrane transporter activity0.0475105037576734
GO:0015296anion:cation symporter activity0.0475105037576734
GO:0007269neurotransmitter secretion0.0475105037576734
GO:0005887integral to plasma membrane0.0475105037576734
GO:0031226intrinsic to plasma membrane0.0475105037576734
GO:0045055regulated secretory pathway0.0475105037576734



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
embryonic stem cell1.74e-075
Uber Anatomy
Ontology termp-valuen
neural tube8.76e-8056
neural rod8.76e-8056
future spinal cord8.76e-8056
neural keel8.76e-8056
regional part of nervous system1.97e-7353
regional part of brain1.97e-7353
nervous system6.51e-7189
central nervous system1.12e-7081
brain2.79e-6368
future brain2.79e-6368
regional part of forebrain2.87e-6241
forebrain2.87e-6241
anterior neural tube2.87e-6241
future forebrain2.87e-6241
telencephalon4.00e-6234
brain grey matter4.47e-6234
gray matter4.47e-6234
cerebral hemisphere4.76e-6232
regional part of telencephalon1.57e-5732
neural plate4.82e-5682
presumptive neural plate4.82e-5682
neurectoderm7.35e-5386
regional part of cerebral cortex6.49e-5122
neocortex3.71e-4620
ecto-epithelium8.83e-46104
cerebral cortex2.87e-4425
pallium2.87e-4425
pre-chordal neural plate3.21e-4461
adult organism4.64e-39114
ectoderm-derived structure5.62e-35171
ectoderm5.62e-35171
presumptive ectoderm5.62e-35171
structure with developmental contribution from neural crest7.45e-35132
organ system subdivision6.74e-28223
tube1.02e-19192
basal ganglion2.29e-199
nuclear complex of neuraxis2.29e-199
aggregate regional part of brain2.29e-199
collection of basal ganglia2.29e-199
cerebral subcortex2.29e-199
neural nucleus6.24e-199
nucleus of brain6.24e-199
posterior neural tube6.78e-1815
chordal neural plate6.78e-1815
gyrus5.44e-166
telencephalic nucleus1.59e-147
anatomical conduit4.83e-14240
limbic system6.86e-145
temporal lobe2.18e-136
anatomical cluster2.33e-13373
parietal lobe3.49e-135
occipital lobe4.28e-135
segmental subdivision of hindbrain2.62e-1212
hindbrain2.62e-1212
presumptive hindbrain2.62e-1212
epithelium2.69e-12306
corpus striatum3.35e-124
striatum3.35e-124
ventral part of telencephalon3.35e-124
future corpus striatum3.35e-124
cell layer4.81e-12309
organ part1.84e-11218
segmental subdivision of nervous system3.01e-1113
brainstem2.32e-106
regional part of metencephalon1.02e-099
metencephalon1.02e-099
future metencephalon1.02e-099
caudate-putamen1.40e-093
dorsal striatum1.40e-093
frontal cortex4.59e-093
pons3.02e-083
spinal cord8.30e-083
dorsal region element8.30e-083
dorsum8.30e-083
embryo1.15e-07592
multi-tissue structure2.64e-07342
caudate nucleus6.27e-072
future caudate nucleus6.27e-072
dorsal plus ventral thalamus9.22e-072
thalamic complex9.22e-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)
MA0003.14.08206
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
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
MA0048.13.56533
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.12.26581
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.11.15845
MA0060.12.90543
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
MA0073.110.33
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
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.11.34409
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
MA0119.10.440684
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
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.11.16614
MA0146.12.38407
MA0147.11.57246
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.23.75773
MA0138.23.01409
MA0002.20.255126
MA0137.20.414885
MA0104.22.08061
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.12.1986
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.12.40092
MA0163.10.508943
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.25.61874
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ETS1#211346.485840614801560.001410474068463220.00917067180702423
HDAC2#306636.707810118313130.006973940027962660.0294902956749693
SIN3A#2594243.605923151210090.01273893844487140.0459470228016273



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:C1482&oldid=2569993"