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Coexpression cluster:C779: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.280498,1.54372,2.11842,0.404877,0.237701,0.403356,2.07596,0.434224,0.429396,1.88248,2.61719,0.515448,0.708134,0.46359,0.236531,0.256724,0.68716,0.191625,0.371758,1.09162,0.274046,0.805814,1.02534,0.233338,0.314616,0.537051,0.0930454,0.39419,0.675066,0.281506,0.935963,0.722879,0.165252,0.352585,1.77252,0.359459,0.593726,1.04333,0.186493,0.395523,0.207288,0.903115,0.127662,0.235234,0.92546,0.814459,1.19689,0.958158,0.279701,0.240465,0.550604,0.486559,0.214602,0.797754,0.947672,1.17737,0.244111,1.94587,0.0825677,1.10913,1.79997,0.477672,0.139078,0.660336,1.23797,0.627106,1.0348,1.4,0.712787,1.2388,0.876593,0.144996,1.22034,0.945703,1.68253,0.316793,0.292851,0.644006,0.709631,0.832314,0.11972,0.659298,0.49429,0.142768,0.89511,6.3077,0.396373,0.272913,0.575506,1.4989,1.12715,0.868602,0.739223,0.171001,0.238337,0.18161,0.368981,1.83708,0.579925,0.896538,0.187593,0.733724,0.775299,0.690713,0.616014,0.970906,1.61879,0.460348,0.844195,1.19204,0.283874,0.772599,0.269151,0.384185,1.07963,0.590599,2.50286,0.354459,0.624851,0.515375,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.260985,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,2.20889,1.15174,2.66605,0.869654,0.821366,0.477214,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.479645,0.473159,1.05336
|tfbs_overrepresentation_jaspar=MA0003.1;1.34002,MA0004.1;0.990587,MA0006.1;0.665232,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;1.9973,MA0017.1;0.270554,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;1.99525,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;1.20033,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;1.25863,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.0662377,MA0056.1;0,MA0057.1;0.802927,MA0058.1;1.44856,MA0059.1;0.291897,MA0060.1;0.848451,MA0061.1;0.118318,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.304755,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;6.11061,MA0074.1;1.19015,MA0076.1;2.28647,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;1.25978,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;1.2478,MA0095.1;0,MA0098.1;0,MA0100.1;1.2287,MA0101.1;0.241637,MA0103.1;0.646502,MA0105.1;0.422512,MA0106.1;0.516528,MA0107.1;0.179177,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;0.532314,MA0114.1;0.51954,MA0115.1;1.06753,MA0116.1;1.02702,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;2.34656,MA0140.1;0.437738,MA0141.1;0.290336,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.163394,MA0145.1;0.14293,MA0146.1;4.09727,MA0147.1;1.64152,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;1.77242,MA0035.2;0.437071,MA0039.2;3.71199,MA0138.2;0.569505,MA0002.2;0.407187,MA0137.2;0.255808,MA0104.2;1.97382,MA0047.2;0.504873,MA0112.2;0.904106,MA0065.2;0.147044,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.185581,MA0155.1;1.25014,MA0156.1;0.715501,MA0157.1;0.612166,MA0158.1;0,MA0159.1;1.04074,MA0160.1;0.417847,MA0161.1;0,MA0162.1;4.5564,MA0163.1;1.66479,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;3.32635,MA0102.2;1.36707,MA0258.1;0.472117,MA0259.1;1.06648,MA0442.1;0
}}
}}

Revision as of 19:26, 22 January 2013


Full id: C779_testis_medial_occipital_brain_temporal_postcentral_insula



Phase1 CAGE Peaks

Hg19::chr10:134145640..134145724,+p1@LRRC27
Hg19::chr11:72504681..72504716,-p6@STARD10
Hg19::chr11:73882263..73882276,+p5@PPME1
Hg19::chr11:73882283..73882309,+p3@PPME1
Hg19::chr12:121341939..121341985,-p3@SPPL3
Hg19::chr12:50101500..50101550,+p23@TMBIM6
Hg19::chr13:37006398..37006417,+p5@CCNA1
Hg19::chr14:105767100..105767153,+p3@PACS2
Hg19::chr15:33486929..33486977,-p5@FMN1
Hg19::chr9:34665983..34666063,-p1@ENST00000416454
p1@ENST00000421828
p1@ENST00000544078
p1@ENST00000556719


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:0051722protein C-terminal methylesterase activity0.00735856827869091
GO:0051723protein methylesterase activity0.00735856827869091
GO:0006482protein amino acid demethylation0.00735856827869091
GO:0008214protein amino acid dealkylation0.00735856827869091
GO:0007141male meiosis I0.00882976206266084
GO:0051721protein phosphatase 2A binding0.00981026913500083
GO:0007140male meiosis0.0147128048027599
GO:0019903protein phosphatase binding0.0312463083769772
GO:0019902phosphatase binding0.0359328864606653
GO:0004864protein phosphatase inhibitor activity0.0428416640546203
GO:0019212phosphatase inhibitor activity0.0428416640546203
GO:0008601protein phosphatase type 2A regulator activity0.0428416640546203



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
nervous system5.77e-3789
central nervous system2.77e-3681
neural tube1.15e-3556
neural rod1.15e-3556
future spinal cord1.15e-3556
neural keel1.15e-3556
regional part of nervous system9.15e-3453
regional part of brain9.15e-3453
brain5.58e-3268
future brain5.58e-3268
neurectoderm3.24e-3186
neural plate5.45e-3082
presumptive neural plate5.45e-3082
adult organism1.39e-29114
regional part of forebrain2.42e-2641
forebrain2.42e-2641
anterior neural tube2.42e-2641
future forebrain2.42e-2641
ectoderm-derived structure1.12e-23171
ectoderm1.12e-23171
presumptive ectoderm1.12e-23171
telencephalon4.60e-2234
brain grey matter6.65e-2234
gray matter6.65e-2234
pre-chordal neural plate9.75e-2261
ecto-epithelium1.66e-21104
cerebral hemisphere7.85e-2132
regional part of telencephalon1.15e-2032
structure with developmental contribution from neural crest1.16e-19132
cerebral cortex2.74e-1625
pallium2.74e-1625
regional part of cerebral cortex4.39e-1622
anatomical cluster7.01e-16373
organ system subdivision1.37e-15223
neocortex9.77e-1520
tube2.26e-12192
multi-cellular organism6.64e-11656
multi-tissue structure1.01e-10342
anatomical conduit1.04e-10240
posterior neural tube2.54e-1015
chordal neural plate2.54e-1015
epithelium4.80e-10306
cell layer7.12e-10309
organ part3.20e-09218
segmental subdivision of hindbrain1.46e-0812
hindbrain1.46e-0812
presumptive hindbrain1.46e-0812
segmental subdivision of nervous system6.95e-0813
anatomical system1.93e-07624
anatomical group2.05e-07625
basal ganglion3.28e-079
nuclear complex of neuraxis3.28e-079
aggregate regional part of brain3.28e-079
collection of basal ganglia3.28e-079
cerebral subcortex3.28e-079
embryo3.84e-07592
neural nucleus4.50e-079
nucleus of brain4.50e-079


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)
MA0003.11.34002
MA0004.10.990587
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.11.9973
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.11.99525
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.11.20033
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.11.25863
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.802927
MA0058.11.44856
MA0059.10.291897
MA0060.10.848451
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.16.11061
MA0074.11.19015
MA0076.12.28647
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.11.25978
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.11.2478
MA0095.10
MA0098.10
MA0100.11.2287
MA0101.10.241637
MA0103.10.646502
MA0105.10.422512
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.11.02702
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.12.34656
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.14.09727
MA0147.11.64152
MA0148.10.403564
MA0149.10.428597
MA0062.21.77242
MA0035.20.437071
MA0039.23.71199
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.21.97382
MA0047.20.504873
MA0112.20.904106
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.185581
MA0155.11.25014
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.10.417847
MA0161.10
MA0162.14.5564
MA0163.11.66479
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.23.32635
MA0102.21.36707
MA0258.10.472117
MA0259.11.06648
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
ATF3#46748.98526981040350.0006636746018777640.00542613995189539
BRCA1#67236.055269192967130.01121625560138660.0411860811037627
CHD2#110666.206413700470110.0001213341309247110.001643794953904
CTCFL#14069035.923942307692310.01190857855768930.0433336830070909
E2F1#186973.435172450415530.0009731854789143080.00699604338052942
E2F4#187456.334030157642220.0005501567218568720.00469848866415978
E2F6#187694.515440158527654.07099158370721e-060.000129546096895429
EGR1#195862.992907456886080.006446587185075730.0280087827199486
ELF1#199772.980668571165280.002378202870469130.0134709366302704
GATA3#262538.17095490716180.004888573999674950.0228754773937924
IRF1#365975.346014627494735.49768438584683e-050.000930587778887289
MAX#414963.871533305404270.001649602786473820.0103163392464994
MXI1#460143.984628651503720.01296562982531040.0460114649448043
MYC#460973.655597310126580.000654500840128410.00535994771757006
NANOG#7992338.77343354430380.004002360774245590.0191876317145483
NRF1#489956.105139723855450.0006527262974630640.00534583451856532
PAX5#507964.00173931870670.001379489661762990.00898599892626862
PRDM1#639226.36619115549220.002484962521039670.0139553154129624
RAD21#588544.142013558182530.01132276475674040.0415275399785508
RDBP#7936230.7276807980050.001839920449249570.0108878379397799
RFX5#599356.023955413597550.0006945114068748440.00559676518692916
SIN3A#2594263.245330836089080.004223840630485730.0201008699356283
SMC3#912646.017973137973140.002957963916685310.0157688118776324
SP1#666773.988866964698630.0003734365591501510.00371123235332407
STAT1#677236.211976249159760.01045841177951960.0387465792068552
TAF1#687272.34013240002170.01040839844348330.0386298054384843
THAP1#5514539.41074338085540.003283183553142890.0170009622245372
USF1#739163.816899566324770.001780928663791640.010926942117127
USF2#739245.196878954027840.005046003840154460.023504731950488
YY1#752862.946702449912310.006987247873951880.0295358068849986



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:C779&oldid=2569290"