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Coexpression cluster:C1165: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.247072,1.00019,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,1.65644,1.24425,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.786991,0.19568,0.0986842,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.164928,1.28759,0.346214,0.150685,0.475674,0.864517,3.71901,0.186138,1.50609,19.2239,3.15467,0.529001,0.282922,9.23685,0.307642,0.459366,0.541549,0.902101,0.0257952,1.06715,1.47235,0.486696,0.0670664,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,8.25698,1.0929,1.01827,0.168304,0.156354,1.84122,0.850825,0.424224,0.200147,0.798651,0.625403,0.649554,1.04131,1.28944,6.85971,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,2.13786,0.815341,0.589207,1.92716,0.327379,0.395884,2.11424,2.63462,0.507004,1.22894,0.304323,1.00084,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,2.08972,1.14174,0.633392,1.28996,1.37933,0.469685,0.518459,2.78754,2.10682,1.70417,1.21002,0.59959,0.920609,2.98295,0.554217,0.738579,1.94751,0.456039,2.05191,0.345641,3.74585,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,1.03728,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692
|tfbs_overrepresentation_for_novel_motifs=1.01633,0.247072,1.00019,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,1.65644,1.24425,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.786991,0.19568,0.0986842,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.164928,1.28759,0.346214,0.150685,0.475674,0.864517,3.71901,0.186138,1.50609,19.2239,3.15467,0.529001,0.282922,9.23685,0.307642,0.459366,0.541549,0.902101,0.0257952,1.06715,1.47235,0.486696,0.0670664,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,8.25698,1.0929,1.01827,0.168304,0.156354,1.84122,0.850825,0.424224,0.200147,0.798651,0.625403,0.649554,1.04131,1.28944,6.85971,0.448771,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,2.13786,0.815341,0.589207,1.92716,0.327379,0.395884,2.11424,2.63462,0.507004,1.22894,0.304323,1.00084,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,2.08972,1.14174,0.633392,1.28996,1.37933,0.469685,0.518459,2.78754,2.10682,1.70417,1.21002,0.59959,0.920609,2.98295,0.554217,0.738579,1.94751,0.456039,2.05191,0.345641,3.74585,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,1.03728,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.0992692
|tfbs_overrepresentation_jaspar=MA0003.1;1.04589,MA0004.1;0.502801,MA0006.1;1.62096,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.187674,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;1.29551,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.382278,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;1.01052,MA0056.1;0,MA0057.1;0.744639,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.638423,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;1.51089,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;3.16596,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.252594,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;1.491,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;1.30855,MA0145.1;1.46178,MA0146.1;0.547931,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.0553061,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.250175,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.25944,MA0163.1;0.19677,MA0164.1;0.678332,MA0080.2;0.911393,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;5.16194,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:44, 22 January 2013


Full id: C1165_occipital_parietal_duodenum_temporal_brain_medial_frontal



Phase1 CAGE Peaks

Hg19::chr12:122459956..122459988,+p3@BCL7A
Hg19::chr5:88036490..88036495,-p@chr5:88036490..88036495
-
Hg19::chr5:88178983..88179012,-p1@MEF2C
Hg19::chr5:88179017..88179046,-p2@MEF2C
Hg19::chr5:88179195..88179224,-p3@MEF2C
Hg19::chr5:88179518..88179569,-p5@MEF2C
Hg19::chr6:62996066..62996137,-p1@KHDRBS2


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:0001958endochondral ossification0.015700393513282
GO:0001974blood vessel remodeling0.015700393513282
GO:0002062chondrocyte differentiation0.015700393513282
GO:0045449regulation of transcription0.015700393513282
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.015700393513282
GO:0006350transcription0.015700393513282
GO:0010468regulation of gene expression0.015700393513282
GO:0031323regulation of cellular metabolic process0.015700393513282
GO:0019222regulation of metabolic process0.0163963732111183
GO:0001649osteoblast differentiation0.0178697429430301
GO:0051216cartilage development0.0233855421719481
GO:0010467gene expression0.0279180613752491
GO:0050794regulation of cellular process0.0294799521563611
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0295006278096016
GO:0050789regulation of biological process0.0318685023796382
GO:0031214biomineral formation0.034238230533469
GO:0001503ossification0.034238230533469
GO:0065007biological regulation0.034238230533469
GO:0007507heart development0.034238230533469
GO:0046849bone remodeling0.034238230533469
GO:0048771tissue remodeling0.0356553666608488
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.045010292622195
GO:0048514blood vessel morphogenesis0.0455204763418833
GO:0001568blood vessel development0.0470817168598508
GO:0001944vasculature development0.0470817168598508
GO:0007517muscle development0.0470817168598508
GO:0003713transcription coactivator activity0.0492700420420545



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism6.19e-43114
neural tube1.56e-2556
neural rod1.56e-2556
future spinal cord1.56e-2556
neural keel1.56e-2556
regional part of nervous system4.82e-2453
regional part of brain4.82e-2453
regional part of forebrain4.40e-2241
forebrain4.40e-2241
anterior neural tube4.40e-2241
future forebrain4.40e-2241
central nervous system3.39e-2181
brain4.64e-1968
future brain4.64e-1968
telencephalon5.41e-1934
brain grey matter1.42e-1834
gray matter1.42e-1834
nervous system2.05e-1889
cerebral hemisphere3.15e-1832
regional part of telencephalon6.38e-1832
regional part of cerebral cortex9.47e-1622
cerebral cortex3.35e-1525
pallium3.35e-1525
neocortex1.08e-1420
neural plate7.40e-1482
presumptive neural plate7.40e-1482
neurectoderm4.43e-1386
tissue9.88e-13773
hemolymphoid system2.93e-11108
hematopoietic system2.44e-1098
blood island2.44e-1098
pre-chordal neural plate2.67e-1061
structure with developmental contribution from neural crest3.13e-09132
immune system1.36e-0893
tube8.14e-08192
ecto-epithelium1.26e-07104
bone element2.00e-0782
bone marrow3.15e-0776
Disease
Ontology termp-valuen
myeloid leukemia1.73e-0731


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)
MA0003.11.04589
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.11.29551
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.11.01052
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.11.51089
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.13.16596
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.11.46178
MA0146.10.547931
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.25944
MA0163.10.19677
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.25.16194
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
ZNF263#1012744.698195221148960.00564122953609810.0254828880415463



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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