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Coexpression cluster:C275: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;5:5.33146605436839:0.00241265506505049:0.0135989682302773
|tf_chipseq_enrich=SUZ12#23512;5:5.33146605436839:0.00241265506505049:0.0135989682302773
|tfbs_overrepresentation=0.00112669,0.0708518,0.685391,0.179029,0.00972738,0.0012392,0.497771,2.34916e-05,0.0966962,0.335013,0.0328794,0.0511773,0.414695,0.163157,0.0148034,0.63252,0.425264,0.22166,0.572879,0.267114,0.0493228,0.652264,0.0471929,0.00539801,0.14381,0.000169424,0.309103,5.17133e-07,0.0375886,0.454036,0.696049,0.000785744,0.248038,0.00448875,0.00501122,0.749088,0.37201,0.151665,0.325753,0.294199,0.471667,0.323217,0.213703,0.103824,0.0543886,0.439165,0.124281,0.040949,0.116591,0.147255,0.125613,0.217534,0.680093,0.0199831,0.00313637,0.126439,0.0350466,0.0147386,0.721347,0.100492,0.373742,0.465232,0.537492,0.350869,0.219889,0.195404,3.02064e-05,0.0747826,0.411635,0.162369,0.219258,0.0991559,0.767984,0.141389,0.110917,0.237002,0.0774042,0.503391,0.120166,0.107775,0.0223159,0.219891,0.493584,0.852103,0.17774,0.304842,0.647216,0.00148826,0.0271857,0.00389871,0.754547,0.190058,0.20904,0.532494,0.407596,0.300183,0.024779,0.0500141,0.00101714,0.387435,0.604471,0.00225082,0.690918,0.446639,0.541586,0.480405,0.295949,0.00040509,0.100938,0.124747,0.00160502,0.103162,0.465865,0.243877,0.235382,0.416038,0.0419311,0.232545,0.089107,0.398403,0.32081,0.0896468,0.0107764,0.167735,0.0919855,0.0361017,0.0180802,0.208238,0.0515773,4.89518e-06,0.618001,0.344084,0.235964,0.303099,0.00595288,0.534867,0.650295,0.590098,0.409254,0.0602004,0.0513989,0.168736,0.288394,0.929846,0.0858963,0.675491,0.484759,0.161323,0.025374,0.146059,0.0100192,0.227574,0.040077,0.000945787,0.495311,0.0151343,0.703978,0.0232633,0.564661,0.415778,0.00879187,0.208598,0.0476619,0.243583,0.0684406,0.0441853,0.135264,0.167918,0.475508,0.00296166,0.0142893,0.000684597,0.0411818,0.217268,0.00227445,0.435086,0.0108644,0.956882,0.19826,0.111627,0.288112,0.60652,0.352966,0.129451,0.0337527,0.00103691,2.52814e-07,0.473977,0.000515116,0.0328344,0.262834,0.408393,0.871915,0.00910782,0.0419039,0.007473,0.364857,0.622486,0.666261,0.111934,0.0613898,0.000524106,0.387763,0.624481,0.00257783,0.691078,0.00204473,0.476604,0.0749163,0.00447482,0.168262,0.0972201,9.23975e-06,0.00322523,0.373142,0.00991043,0.532952,0.00730998,0.639181,0.507619,0.691142,0.121144,0.00605764,0.0608931,0.0339514,0.0642164,0.209244,0.0145858,0.623536,0.620024,0.00120683,0.147429,0.48809,0.037978,0.0056914,0.453035,0.531367,0.00388244,0.307391,0.524165,6.00091e-06,0.142718,0.0819878,0.0492159,0.000895689,0.00947354,0.736065,0.00302482,0.00362452,0.580261,0.00681663,0.0170545,0.00183898,0.801382,0.480682,0.140903,0.0347824,0.00353266,0.676941,0.0071999,0.264773,0.187387,0.0241929,0.632453,0.10581,0.734065,0.382411,0.77978,0.860339,0.348242,0.403464,0.273196,0.675441,0.145069,0.0558846,0.124439,0.177688,0.157175,0.0423196,0.0934297,0.0530594,0.107942,0.256801,0.0693034,0.0614881,7.96828e-09,0.698148,0.0877733,0.0367723,0.000117228,0.0423456,0.00218653,0.00326862,9.57396e-06,2.21827e-05,0.0110353,0.00066252,0.00391228,1.63338e-06,9.98022e-06,0.000921523,0.000819985,0.0476123,0.0561217,0.384519,0.365526,0.838859,0.00544962,5.25445e-05,5.16517e-06,9.48806e-05,0.000503436,0.0165475,0.0178516,0.0266377,0.000547097,4.52628e-10,0.164885,0.0934766,1.0419e-07,7.37847e-06,0.00223531,0.000483269,0.0202843,0.00449225,0.0631344,0.893274,0.0183801,0.00162134,0.000501179,0.00739222,0.00156193,0.0493965,0.0100025,0.0082923,9.85596e-06,8.27695e-05,5.19597e-06,0.308183,0.6105,0.00461589,0.0778225,0.0132847,0.741334,0.00426252,0.83108,0.00147998,0.0378371,0.000204397,0.0254641,0.00892102,0.00623428,6.95793e-09,0.00231408,0.264718,0.000302699,0.0080039,0.0970451,0.118166,0.00572442,0.00319919,0.199264,0.000201436,0.045419,0.00210524,3.82104e-08,0.000598801,0.000276102,0.00649061,3.84313e-06,0.015387,0.163881,0.0352814,0.00325639,0.158719,0.00891161,0.00434305,0.0105622,0.0176671,6.04087e-05,0.0462776,0.000724349,0.0685201,0.0750995,0.17652,0.00880834,0.116594,1.17256e-06,0.135793,0.0017451,0.00110756,0.000235691,1.12067e-05,0.0940287,0.11451,0.709128,0.0610931,0.00377831,0.234781,0.00232745,3.16122e-05,0.0146525,1.2078e-07,0.000282865,0.263047,0.17235,0.202711,0.000118022,0.661755,0.0824441,0.0786537,0.000180174,0.274725,0.00802498,0.00031527,0.00606898,0.0945613,0.0902845,2.02601e-10,0.00109702,0.00134897,0.268109,0.000285965,0.0201163,1.27971e-10,0.00632544,9.64927e-11,0.00361236,0.158402,0.617908,0.0491014,2.47321e-05,0.36893,0.00292518,0.0101412,0.00708079,0.000849543,0.610648,0.000384863,0.140743,0.0045905,0.0678366,0.00122126,0.00215665,0.429615,0.250294,0.132221,1.21753e-05,0.230728,0.000367018,0.144713,3.05615e-08,0.000115367,0.0134975,0.0054079,0.0190808,0.677947,0.592455,0.650632,0.009789,0.238105,0.230063,0.106632,0.0110655,0.434283,0.0247245,0.00738306,0.844285,0.172519,0.154902,0.0302096,0.0639752,0.194458,0.26164,0.000700661,0.270123,0.8697,0.246584,0.341862,9.47965e-05,0.885399,0.0071502,0.945615,0.851413,0.250772,0.434359,0.0150888,0.141343,0.104713,0.504768,0.0592438,0.15513,0.174117,0.00485104,0.250726,0.136922,0.00920317,0.742233,0.0243881,0.00157616,0.842479,0.000707517,0.0582955,0.008438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|tfbs_overrepresentation_for_novel_motifs=0.335895,0.078683,1.14994,0.675304,0.931569,1.04006,0.520292,0.804138,0.244529,1.44157,0.138628,0.292222,0.0761553,0.497453,0.235381,0.480743,0.53149,0.666712,0.0420535,2.79211,1.5302,0.246024,0.362681,0.228593,0.0875587,1.61336,1.02789,0.643635,1.65749,0.503947,0.288551,0.586391,0.746629,0.384442,1.04908,0.50844,0.0255924,0.0433158,0.138268,0.200059,0.0797051,0.491702,0.0962205,0.232614,0.197206,0.199506,0.0692392,0.0318343,0.185537,0.11647,0.103211,0.0738553,1.41326,0.253654,1.70825,0.233244,0.120904,0.0539437,0.355346,0.438066,0.229344,0.070154,0.390148,0.163473,0.0772948,0.869884,0.436932,0.759916,0.196165,0.61311,0.74346,0.266654,0.119674,0.364729,0.23029,0.30678,0.541636,0.153778,0.194134,0.668746,0.635675,0.16285,0.563004,0.147351,0.325376,0.0480184,0.198252,0.646183,0.115837,0.852295,0.515064,0.305295,0.611992,0.112632,1.26577,0.406541,0.0901543,0.678272,0.118145,0.53622,1.53529,1.78011,0.237959,0.536884,0.426921,0.134809,0.988886,0.490674,0.219958,0.0975387,0.344113,0.236094,0.523844,0.340172,0.474484,0.170788,0.675719,0.529583,0.142715,0.116277,0.358301,1.21572,0.371469,0.586337,0.569162,0.912971,0.507641,0.619662,0.391733,0.131249,0.305804,0.539947,1.04066,0.579412,0.526085,0.0652761,0.279082,0.0402617,0.489984,1.28951,0.901617,0.458761,0.0670595,0.672713,1.97609,0.744387,0.406701,1.13449,0.483494,0.210279,0.0959776,0.0251493,0.306085,0.0597614,0.526252,1.54574,0.107906,0.212898,0.0875978,0.181327,0.457752,0.292546,0.193642,0.605012,2.04687,0.951453,0.185665,2.42939,0.0410928
}}
}}

Revision as of 14:00, 26 November 2012


Full id: C275_pons_medulla_cerebellum_locus_thalamus_diencephalon_spinal



Phase1 CAGE Peaks

Hg19::chr10:17045960..17045970,-p@chr10:17045960..17045970
-
Hg19::chr10:61043434..61043446,-p13@FAM13C
Hg19::chr10:61043452..61043467,-p16@FAM13C
Hg19::chr11:22359520..22359556,+p3@SLC17A6
Hg19::chr11:22359562..22359575,+p6@SLC17A6
Hg19::chr11:22359879..22359909,+p2@SLC17A6
Hg19::chr11:3224761..3224787,-p@chr11:3224761..3224787
-
Hg19::chr11:3224982..3224985,-p@chr11:3224982..3224985
-
Hg19::chr11:3224990..3225000,-p@chr11:3224990..3225000
-
Hg19::chr11:3253592..3253608,-p2@MRGPRE
Hg19::chr11:3253635..3253658,-p1@MRGPRE
Hg19::chr11:3253663..3253670,-p4@MRGPRE
Hg19::chr11:3253872..3253882,-p3@MRGPRE
Hg19::chr12:33592574..33592584,-p6@SYT10
Hg19::chr13:93587956..93587973,+p@chr13:93587956..93587973
+
Hg19::chr16:47920709..47920716,-p4@uc002eex.1
Hg19::chr16:49669972..49669983,-p@chr16:49669972..49669983
-
Hg19::chr16:49670005..49670020,-p@chr16:49670005..49670020
-
Hg19::chr16:67237164..67237171,+p@chr16:67237164..67237171
+
Hg19::chr17:68101117..68101162,+p2@KCNJ16
Hg19::chr1:205313500..205313511,-p11@KLHDC8A
Hg19::chr1:216692584..216692595,-p@chr1:216692584..216692595
-
Hg19::chr1:216692717..216692725,-p@chr1:216692717..216692725
-
Hg19::chr1:216692728..216692741,-p@chr1:216692728..216692741
-
Hg19::chr1:218222373..218222381,-p@chr1:218222373..218222381
-
Hg19::chr1:218222386..218222394,-p@chr1:218222386..218222394
-
Hg19::chr21:31312092..31312103,-p7@GRIK1
Hg19::chr2:17381145..17381164,-p@chr2:17381145..17381164
-
Hg19::chr2:72381655..72381673,-p@chr2:72381655..72381673
-
Hg19::chr4:117675601..117675614,+p@chr4:117675601..117675614
+
Hg19::chr4:117675642..117675654,+p@chr4:117675642..117675654
+
Hg19::chr4:186661365..186661384,-p46@SORBS2
Hg19::chr4:82965824..82965835,-p6@ENST00000508294
p6@ENST00000510780
p6@ENST00000512343
p6@ENST00000512716
p6@ENST00000514050
Hg19::chr5:126959224..126959239,+p@chr5:126959224..126959239
+
Hg19::chr5:126959900..126959932,+p@chr5:126959900..126959932
+
Hg19::chr5:126959946..126959960,+p@chr5:126959946..126959960
+
Hg19::chr6:140415977..140415987,-p@chr6:140415977..140415987
-
Hg19::chr6:140415989..140415997,-p@chr6:140415989..140415997
-
Hg19::chr6:140416018..140416025,-p@chr6:140416018..140416025
-
Hg19::chr6:71665623..71665630,-p13@B3GAT2
Hg19::chr7:31569075..31569083,+p3@CCDC129
Hg19::chr7:31569365..31569379,+p1@CCDC129
Hg19::chr9:135457530..135457541,+p2@BARHL1
Hg19::chr9:135457972..135457978,+p8@BARHL1
Hg19::chr9:135458021..135458030,+p6@BARHL1
Hg19::chr9:135458288..135458301,+p3@BARHL1
Hg19::chr9:135458306..135458314,+p9@BARHL1


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:0051966regulation of synaptic transmission, glutamatergic0.0414160162571539
GO:0035249synaptic transmission, glutamatergic0.0414160162571539
GO:0016021integral to membrane0.0414160162571539
GO:0031224intrinsic to membrane0.0414160162571539
GO:0051179localization0.0414160162571539
GO:0015018galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity0.0414160162571539
GO:0015277kainate selective glutamate receptor activity0.0414160162571539
GO:0044425membrane part0.04833425076599



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
brainstem7.67e-1036
pons1.66e-743
segmental subdivision of hindbrain6.69e-7412
hindbrain6.69e-7412
presumptive hindbrain6.69e-7412
segmental subdivision of nervous system2.95e-6813
posterior neural tube3.20e-5915
chordal neural plate3.20e-5915
locus ceruleus5.15e-502
brainstem nucleus5.15e-502
hindbrain nucleus5.15e-502
regional part of metencephalon3.55e-449
metencephalon3.55e-449
future metencephalon3.55e-449
medulla oblongata3.94e-343
myelencephalon3.94e-343
future myelencephalon3.94e-343
regional part of nervous system3.04e-2953
regional part of brain3.04e-2953
neural tube1.03e-2756
neural rod1.03e-2756
future spinal cord1.03e-2756
neural keel1.03e-2756
paracentral gyrus5.93e-261
nucleus accumbens1.26e-251
ventral striatum1.26e-251
neural nucleus3.17e-259
nucleus of brain3.17e-259
brain1.35e-2268
future brain1.35e-2268
central nervous system4.48e-1981
neural plate4.48e-1982
presumptive neural plate4.48e-1982
neurectoderm3.34e-1886
nervous system3.23e-1789
ecto-epithelium4.31e-15104
adult organism6.68e-14114
structure with developmental contribution from neural crest6.49e-12132
organ segment3.13e-0998
ectoderm-derived structure4.33e-09171
ectoderm4.33e-09171
presumptive ectoderm4.33e-09171
tube3.49e-08192
corpus striatum2.04e-074
striatum2.04e-074
ventral part of telencephalon2.04e-074
future corpus striatum2.04e-074
organ part3.42e-07218
brain grey matter5.30e-0734
gray matter5.30e-0734
organ system subdivision6.23e-07223


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)

{{{tfbs_overrepresentation_jaspar}}}



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#2351255.331466054368390.002412655065050490.0135989682302773



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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