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Coexpression cluster:C257: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.481682,0.182427,1.35691,0.0352482,0.551135,0.0348237,0.460917,0.474616,0.463501,1.14101,0.514979,0.256585,1.02514,0.0538303,0.087353,0.230197,0.48452,0.791812,0.0657141,1.54744,0.709211,0.0705532,0.571653,1.07202,0.182796,1.48337,0.477188,0.309568,1.12048,1.14967,1.49707,0.182397,0.855791,0.109304,0.432084,0.525996,0.421678,1.33913,0.348556,1.25369,0.0603441,0.692178,0.220881,0.790221,0.96613,0.327431,0.211382,0.261018,0.0466274,0.355091,1.04071,0.485536,0.586922,0.231144,0.901894,0.775962,1.14655,0.684497,0.174273,0.681743,1.12906,0.21381,0.656188,0.875041,0.862736,0.126911,0.409209,0.727856,0.176167,0.58255,1.75396,0.0202535,0.569379,0.898518,0.985457,0.673517,0.192655,0.422759,0.517685,0.0665908,0.515445,0.144625,0.501417,0.110639,0.300427,1.46476,8.05119,0.16143,1.1222,0.819547,0.485902,0.280966,0.562326,1.17868,0.807344,0.33076,0.483682,0.62667,0.687073,0.415468,0.107975,0.189185,0.216077,0.162843,0.77,0.111808,0.46739,0.195261,0.895176,1.00889,0.753591,0.214289,0.444586,0.0297234,0.446027,0.416569,0.888323,0.459063,1.2873,0.918784,1.5895,0.327579,1.77908,0.895026,0.539181,0.136492,0.448951,0.569761,0.365014,0.041432,0.769699,0.46874,0.98155,3.05896,1.2425,2.10452,0.0950578,0.310482,0.461248,1.25501,0.868564,1.10023,0.205577,1.16621,0.773946,0.370366,0.113636,1.10041,0.68118,0.880212,0.10847,0.926042,0.770319,1.34637,0.213312,0.609476,0.0933429,0.312009,0.0701495,0.776942,1.92544,0.268633,0.516545,1.90093,0.407726,0.064938,0.069577,0.208912,0.105684
|tfbs_overrepresentation_for_novel_motifs=0.481682,0.182427,1.35691,0.0352482,0.551135,0.0348237,0.460917,0.474616,0.463501,1.14101,0.514979,0.256585,1.02514,0.0538303,0.087353,0.230197,0.48452,0.791812,0.0657141,1.54744,0.709211,0.0705532,0.571653,1.07202,0.182796,1.48337,0.477188,0.309568,1.12048,1.14967,1.49707,0.182397,0.855791,0.109304,0.432084,0.525996,0.421678,1.33913,0.348556,1.25369,0.0603441,0.692178,0.220881,0.790221,0.96613,0.327431,0.211382,0.261018,0.0466274,0.355091,1.04071,0.485536,0.586922,0.231144,0.901894,0.775962,1.14655,0.684497,0.174273,0.681743,1.12906,0.21381,0.656188,0.875041,0.862736,0.126911,0.409209,0.727856,0.176167,0.58255,1.75396,0.0202535,0.569379,0.898518,0.985457,0.673517,0.192655,0.422759,0.517685,0.0665908,0.515445,0.144625,0.501417,0.110639,0.300427,1.46476,8.05119,0.16143,1.1222,0.819547,0.485902,0.280966,0.562326,1.17868,0.807344,0.33076,0.483682,0.62667,0.687073,0.415468,0.107975,0.189185,0.216077,0.162843,0.77,0.111808,0.46739,0.195261,0.895176,1.00889,0.753591,0.214289,0.444586,0.0297234,0.446027,0.416569,0.888323,0.459063,1.2873,0.918784,1.5895,0.327579,1.77908,0.895026,0.539181,0.136492,0.448951,0.569761,0.365014,0.041432,0.769699,0.46874,0.98155,3.05896,1.2425,2.10452,0.0950578,0.310482,0.461248,1.25501,0.868564,1.10023,0.205577,1.16621,0.773946,0.370366,0.113636,1.10041,0.68118,0.880212,0.10847,0.926042,0.770319,1.34637,0.213312,0.609476,0.0933429,0.312009,0.0701495,0.776942,1.92544,0.268633,0.516545,1.90093,0.407726,0.064938,0.069577,0.208912,0.105684
|tfbs_overrepresentation_jaspar=MA0003.1;1.09077,MA0004.1;0.0287532,MA0006.1;1.0913,MA0007.1;0.024623,MA0009.1;0.252434,MA0014.1;1.10637,MA0017.1;0.449123,MA0019.1;0.262257,MA0024.1;0.183969,MA0025.1;0.924278,MA0027.1;1.73105,MA0028.1;0.0348968,MA0029.1;1.70342,MA0030.1;0.188804,MA0031.1;0.459469,MA0038.1;0.466212,MA0040.1;0.199633,MA0041.1;0.315593,MA0042.1;0.494507,MA0043.1;0.703596,MA0046.1;0.24494,MA0048.1;2.0031,MA0050.1;0.266168,MA0051.1;0.208758,MA0052.1;0.584895,MA0055.1;2.89552,MA0056.1;0,MA0057.1;0.21116,MA0058.1;0.0116659,MA0059.1;0.0561949,MA0060.1;0.189747,MA0061.1;0.0687895,MA0063.1;0,MA0066.1;0.467033,MA0067.1;0.49981,MA0068.1;0.0133684,MA0069.1;0.242306,MA0070.1;0.234718,MA0071.1;0.0459331,MA0072.1;0.231695,MA0073.1;0.0734142,MA0074.1;0.0569489,MA0076.1;0.172646,MA0077.1;0.226543,MA0078.1;0.321356,MA0081.1;0.0562791,MA0083.1;0.25765,MA0084.1;0.664025,MA0087.1;0.230056,MA0088.1;0.148712,MA0089.1;0,MA0090.1;0.191226,MA0091.1;0.289788,MA0092.1;0.441881,MA0093.1;0.00542575,MA0095.1;0,MA0098.1;0,MA0100.1;0.227752,MA0101.1;0.0925848,MA0103.1;0.751317,MA0105.1;0.245901,MA0106.1;0.547964,MA0107.1;0.188877,MA0108.2;0.45517,MA0109.1;0,MA0111.1;0.0183152,MA0113.1;0.0808928,MA0114.1;0.0901948,MA0115.1;0.436009,MA0116.1;0.0999453,MA0117.1;0.763914,MA0119.1;0.00956314,MA0122.1;0.806534,MA0124.1;1.03875,MA0125.1;0.336564,MA0130.1;0,MA0131.1;0.344065,MA0132.1;0,MA0133.1;0,MA0135.1;0.27375,MA0136.1;0.0611972,MA0139.1;0.190948,MA0140.1;1.51094,MA0141.1;0.149727,MA0142.1;1.9318,MA0143.1;0.0809666,MA0144.1;0.152804,MA0145.1;0.277096,MA0146.1;0.0117386,MA0147.1;0.202787,MA0148.1;0.139589,MA0149.1;0.0422402,MA0062.2;0.0271799,MA0035.2;1.06475,MA0039.2;0.00704105,MA0138.2;0.663608,MA0002.2;0.0875896,MA0137.2;0.228332,MA0104.2;0.187993,MA0047.2;0.0694194,MA0112.2;0.16744,MA0065.2;0.0514181,MA0150.1;0.183535,MA0151.1;0,MA0152.1;0.178362,MA0153.1;0.323801,MA0154.1;0.0975962,MA0155.1;1.38924,MA0156.1;0.0383917,MA0157.1;0.76104,MA0158.1;0,MA0159.1;0.344759,MA0160.1;0.0389843,MA0161.1;0,MA0162.1;1.4248,MA0163.1;0.542758,MA0164.1;0.0861719,MA0080.2;0.00543232,MA0018.2;0.935667,MA0099.2;0.0472524,MA0079.2;0.537472,MA0102.2;0.697711,MA0258.1;0.13646,MA0259.1;1.06715,MA0442.1;0
}}
}}

Revision as of 18:53, 22 January 2013


Full id: C257_pineal_insula_frontal_occipital_temporal_medial_paracentral



Phase1 CAGE Peaks

Hg19::chr11:107462012..107462019,+p5@ELMOD1
Hg19::chr11:73309049..73309054,-p5@FAM168A
Hg19::chr11:74952393..74952412,+p@chr11:74952393..74952412
+
Hg19::chr11:795358..795372,-p9@SLC25A22
Hg19::chr11:84148843..84148867,-p21@DLG2
Hg19::chr11:84148869..84148881,-p35@DLG2
Hg19::chr12:130303241..130303258,-p@chr12:130303241..130303258
-
Hg19::chr12:57735443..57735464,-p18@R3HDM2
Hg19::chr12:57735499..57735520,-p10@R3HDM2
Hg19::chr12:57736218..57736229,-p@chr12:57736218..57736229
-
Hg19::chr12:57736233..57736245,-p@chr12:57736233..57736245
-
Hg19::chr12:81992111..81992164,-p1@PPFIA2
Hg19::chr14:72399114..72399238,+p1@RGS6
Hg19::chr19:46580848..46580895,-p1@ENST00000366172
p1@uc002pdz.1
Hg19::chr1:110082487..110082535,+p1@GPR61
Hg19::chr1:177133980..177133992,-p7@ASTN1
Hg19::chr1:204640767..204640771,-p@chr1:204640767..204640771
-
Hg19::chr1:217262933..217262968,-p3@ESRRG
Hg19::chr1:217262969..217262995,-p7@ESRRG
Hg19::chr1:50489619..50489650,-p2@AGBL4
Hg19::chr1:77334255..77334267,+p7@ST6GALNAC5
Hg19::chr2:210444126..210444140,+p14@MAP2
Hg19::chr2:210444142..210444194,+p6@MAP2
Hg19::chr2:215275814..215275834,+p1@VWC2L
Hg19::chr2:219824420..219824431,+p3@CDK5R2
Hg19::chr2:220174072..220174149,-p1@PTPRN
Hg19::chr2:48667898..48667981,+p1@PPP1R21
Hg19::chr2:50574708..50574743,-p17@NRXN1
Hg19::chr3:118753716..118753731,-p7@IGSF11
Hg19::chr3:124103560..124103577,+p8@KALRN
Hg19::chr3:127347780..127347822,-p@chr3:127347780..127347822
-
Hg19::chr3:158991085..158991096,+p26@SCHIP1
Hg19::chr3:64211112..64211152,-p4@PRICKLE2
Hg19::chr3:64211156..64211179,-p11@PRICKLE2
Hg19::chr5:138210931..138210938,-p6@LRRTM2
Hg19::chr5:138210954..138210965,-p4@LRRTM2
Hg19::chr5:138210977..138210999,-p2@LRRTM2
Hg19::chr5:146435485..146435499,-p8@PPP2R2B
Hg19::chr5:146435501..146435530,-p3@PPP2R2B
Hg19::chr5:146435572..146435581,-p24@PPP2R2B
Hg19::chr5:161494848..161494859,+p9@GABRG2
Hg19::chr5:161494946..161494955,+p10@GABRG2
Hg19::chr5:161494956..161494967,+p8@GABRG2
Hg19::chr5:71403323..71403340,+p3@MAP1B
Hg19::chr5:74162339..74162405,-p2@FAM169A
Hg19::chr6:84418484..84418496,-p3@SNAP91
Hg19::chr7:14942830..14942867,-p4@DGKB
Hg19::chr7:14942923..14942941,-p6@DGKB
Hg19::chr7:31023427..31023491,+p1@GHRHR
Hg19::chr7:39125494..39125510,+p4@POU6F2
Hg19::chr7:39125511..39125560,+p1@POU6F2


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:0031114regulation of microtubule depolymerization0.0132628609623142
GO:0007026negative regulation of microtubule depolymerization0.0132628609623142
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0132628609623142
GO:0007019microtubule depolymerization0.0132628609623142
GO:0031110regulation of microtubule polymerization or depolymerization0.015800510186969
GO:0031109microtubule polymerization or depolymerization0.015800510186969
GO:0044464cell part0.015800510186969
GO:0051261protein depolymerization0.0261605814414009
GO:0005515protein binding0.0261605814414009
GO:0051129negative regulation of cellular component organization and biogenesis0.0261605814414009
GO:0007402ganglion mother cell fate determination0.0261605814414009
GO:0016533cyclin-dependent protein kinase 5 activator complex0.0410943584387354
GO:0048664neuron fate determination0.0410943584387354
GO:0016534cyclin-dependent protein kinase 5 activator activity0.0410943584387354



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 tube9.43e-13156
neural rod9.43e-13156
future spinal cord9.43e-13156
neural keel9.43e-13156
regional part of nervous system3.49e-12253
regional part of brain3.49e-12253
central nervous system5.46e-11481
brain6.41e-10568
future brain6.41e-10568
regional part of forebrain7.22e-10441
forebrain7.22e-10441
anterior neural tube7.22e-10441
future forebrain7.22e-10441
nervous system1.35e-10189
neural plate2.45e-9382
presumptive neural plate2.45e-9382
neurectoderm1.76e-8886
telencephalon6.17e-8334
brain grey matter7.77e-8334
gray matter7.77e-8334
cerebral hemisphere1.09e-7732
regional part of telencephalon4.80e-7732
pre-chordal neural plate1.77e-7461
ecto-epithelium3.35e-71104
regional part of cerebral cortex1.69e-6522
adult organism3.93e-62114
structure with developmental contribution from neural crest7.47e-61132
neocortex1.17e-5920
cerebral cortex3.25e-5725
pallium3.25e-5725
ectoderm-derived structure1.17e-51171
ectoderm1.17e-51171
presumptive ectoderm1.17e-51171
organ system subdivision1.00e-36223
tube1.51e-31192
basal ganglion4.06e-279
nuclear complex of neuraxis4.06e-279
aggregate regional part of brain4.06e-279
collection of basal ganglia4.06e-279
cerebral subcortex4.06e-279
neural nucleus1.13e-269
nucleus of brain1.13e-269
posterior neural tube1.18e-2615
chordal neural plate1.18e-2615
anatomical conduit7.79e-23240
diencephalon1.05e-217
future diencephalon1.05e-217
telencephalic nucleus4.39e-217
gyrus1.03e-206
anatomical cluster1.11e-19373
segmental subdivision of hindbrain3.90e-1912
hindbrain3.90e-1912
presumptive hindbrain3.90e-1912
brainstem4.73e-186
segmental subdivision of nervous system1.56e-1713
epithelium3.73e-17306
cell layer7.21e-17309
temporal lobe7.42e-176
parietal lobe8.02e-175
limbic system1.39e-165
occipital lobe1.58e-165
organ part1.56e-14218
regional part of diencephalon1.21e-134
gland of diencephalon1.78e-134
neuroendocrine gland1.78e-134
corpus striatum2.46e-134
striatum2.46e-134
ventral part of telencephalon2.46e-134
future corpus striatum2.46e-134
multi-tissue structure3.27e-13342
regional part of metencephalon6.04e-129
metencephalon6.04e-129
future metencephalon6.04e-129
frontal cortex2.28e-113
pons3.20e-103
caudate-putamen3.30e-103
dorsal striatum3.30e-103
organ9.06e-10503
spinal cord1.33e-093
dorsal region element1.33e-093
dorsum1.33e-093
medulla oblongata1.51e-093
myelencephalon1.51e-093
future myelencephalon1.51e-093
embryo1.14e-08592
germ layer1.27e-08560
germ layer / neural crest1.27e-08560
embryonic tissue1.27e-08560
presumptive structure1.27e-08560
germ layer / neural crest derived structure1.27e-08560
epiblast (generic)1.27e-08560
embryonic structure1.83e-08564
pineal body3.06e-082
regional part of epithalamus3.06e-082
secretory circumventricular organ3.06e-082
circumventricular organ3.06e-082
epithalamus3.06e-082
middle frontal gyrus4.16e-082
middle temporal gyrus5.45e-082
developing anatomical structure8.08e-08581


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)
MA0003.11.09077
MA0004.10.0287532
MA0006.11.0913
MA0007.10.024623
MA0009.10.252434
MA0014.11.10637
MA0017.10.449123
MA0019.10.262257
MA0024.10.183969
MA0025.10.924278
MA0027.11.73105
MA0028.10.0348968
MA0029.11.70342
MA0030.10.188804
MA0031.10.459469
MA0038.10.466212
MA0040.10.199633
MA0041.10.315593
MA0042.10.494507
MA0043.10.703596
MA0046.10.24494
MA0048.12.0031
MA0050.10.266168
MA0051.10.208758
MA0052.10.584895
MA0055.12.89552
MA0056.10
MA0057.10.21116
MA0058.10.0116659
MA0059.10.0561949
MA0060.10.189747
MA0061.10.0687895
MA0063.10
MA0066.10.467033
MA0067.10.49981
MA0068.10.0133684
MA0069.10.242306
MA0070.10.234718
MA0071.10.0459331
MA0072.10.231695
MA0073.10.0734142
MA0074.10.0569489
MA0076.10.172646
MA0077.10.226543
MA0078.10.321356
MA0081.10.0562791
MA0083.10.25765
MA0084.10.664025
MA0087.10.230056
MA0088.10.148712
MA0089.10
MA0090.10.191226
MA0091.10.289788
MA0092.10.441881
MA0093.10.00542575
MA0095.10
MA0098.10
MA0100.10.227752
MA0101.10.0925848
MA0103.10.751317
MA0105.10.245901
MA0106.10.547964
MA0107.10.188877
MA0108.20.45517
MA0109.10
MA0111.10.0183152
MA0113.10.0808928
MA0114.10.0901948
MA0115.10.436009
MA0116.10.0999453
MA0117.10.763914
MA0119.10.00956314
MA0122.10.806534
MA0124.11.03875
MA0125.10.336564
MA0130.10
MA0131.10.344065
MA0132.10
MA0133.10
MA0135.10.27375
MA0136.10.0611972
MA0139.10.190948
MA0140.11.51094
MA0141.10.149727
MA0142.11.9318
MA0143.10.0809666
MA0144.10.152804
MA0145.10.277096
MA0146.10.0117386
MA0147.10.202787
MA0148.10.139589
MA0149.10.0422402
MA0062.20.0271799
MA0035.21.06475
MA0039.20.00704105
MA0138.20.663608
MA0002.20.0875896
MA0137.20.228332
MA0104.20.187993
MA0047.20.0694194
MA0112.20.16744
MA0065.20.0514181
MA0150.10.183535
MA0151.10
MA0152.10.178362
MA0153.10.323801
MA0154.10.0975962
MA0155.11.38924
MA0156.10.0383917
MA0157.10.76104
MA0158.10
MA0159.10.344759
MA0160.10.0389843
MA0161.10
MA0162.11.4248
MA0163.10.542758
MA0164.10.0861719
MA0080.20.00543232
MA0018.20.935667
MA0099.20.0472524
MA0079.20.537472
MA0102.20.697711
MA0258.10.13646
MA0259.11.06715
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
CTBP2#148844.918980418770830.008892658221884340.0337343479000174
RAD21#5885112.233438683333720.008451433748749080.0328004195200894



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

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