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Coexpression cluster:C333: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0335278,0.503913,0.0315461,0.0827999,0.234998,0.990437,0.118779,0.0828962,0.0805298,0.719699,0.0693241,4.25147,0.0460047,0.362753,1.45108,0.503988,0.257271,0.313037,0.242777,0.74284,0.304513,0.893817,0.0786989,0.0205891,0.0449326,0.155544,0.166469,0.0777687,0.0223025,0.560971,0.0607764,1.41493,0.00781483,0.113069,0.0151133,4.65557,0.0145834,0.994178,0.147686,0.274911,0.0148805,0.201531,0.146395,1.88442,0.00201236,0.0402441,0.379777,0.0650089,0.0699262,1.47917,0.163986,0.39595,0.524535,0.341781,0.465668,0.114332,0.751842,0.66477,0.776469,0.097567,2.32079,0.768011,1.74911,0.669291,1.31587,0.614469,0.541393,0.877654,0.27623,2.89123,0.0501811,0.0884386,0.000298886,0.463985,0.00195158,0.465944,0.596164,0.226306,0.273874,0.165441,0.254751,0.237135,0.407306,0.187244,0.421204,8.4053e-07,0.544447,2.68231,0.179915,0.972115,0.623955,0.399177,0.296201,0.690749,0.0951045,0.489489,1.80769,0.328351,0.182797,0.182467,0.301988,0.292013,0.324084,2.85549,1.12551,0.0675056,0.24869,0.358136,0.0448514,0.0184517,0.138608,0.321972,0.123819,0.0731861,0.581207,0.0673661,0.000883454,0.0603238,0.610788,0.263688,0.457029,0.178405,0.981541,0.136233,1.62959,0.226822,6.38702,0.299917,0.493083,0.010379,0.399737,0.0618629,12.4428,0.134387,0.63552,0.000699397,0.0585377,2.58312,0.597567,1.41464,1.02236,0.564569,0.749095,0.325651,2.49995,5.89623,1.08743,1.25835,0.765647,0.00825106,0.621095,0.000305538,0.400046,0.0732975,1.25288,0.754525,0.169944,0.0188349,0.171594,0.1439,0.5635,0.385113,0.273303,0.0371315,1.17143,0.129597,1.9919,0.376484,2.70588e-06
|tfbs_overrepresentation_for_novel_motifs=0.0335278,0.503913,0.0315461,0.0827999,0.234998,0.990437,0.118779,0.0828962,0.0805298,0.719699,0.0693241,4.25147,0.0460047,0.362753,1.45108,0.503988,0.257271,0.313037,0.242777,0.74284,0.304513,0.893817,0.0786989,0.0205891,0.0449326,0.155544,0.166469,0.0777687,0.0223025,0.560971,0.0607764,1.41493,0.00781483,0.113069,0.0151133,4.65557,0.0145834,0.994178,0.147686,0.274911,0.0148805,0.201531,0.146395,1.88442,0.00201236,0.0402441,0.379777,0.0650089,0.0699262,1.47917,0.163986,0.39595,0.524535,0.341781,0.465668,0.114332,0.751842,0.66477,0.776469,0.097567,2.32079,0.768011,1.74911,0.669291,1.31587,0.614469,0.541393,0.877654,0.27623,2.89123,0.0501811,0.0884386,0.000298886,0.463985,0.00195158,0.465944,0.596164,0.226306,0.273874,0.165441,0.254751,0.237135,0.407306,0.187244,0.421204,8.4053e-07,0.544447,2.68231,0.179915,0.972115,0.623955,0.399177,0.296201,0.690749,0.0951045,0.489489,1.80769,0.328351,0.182797,0.182467,0.301988,0.292013,0.324084,2.85549,1.12551,0.0675056,0.24869,0.358136,0.0448514,0.0184517,0.138608,0.321972,0.123819,0.0731861,0.581207,0.0673661,0.000883454,0.0603238,0.610788,0.263688,0.457029,0.178405,0.981541,0.136233,1.62959,0.226822,6.38702,0.299917,0.493083,0.010379,0.399737,0.0618629,12.4428,0.134387,0.63552,0.000699397,0.0585377,2.58312,0.597567,1.41464,1.02236,0.564569,0.749095,0.325651,2.49995,5.89623,1.08743,1.25835,0.765647,0.00825106,0.621095,0.000305538,0.400046,0.0732975,1.25288,0.754525,0.169944,0.0188349,0.171594,0.1439,0.5635,0.385113,0.273303,0.0371315,1.17143,0.129597,1.9919,0.376484,2.70588e-06
|tfbs_overrepresentation_jaspar=MA0003.1;4.93725e-10,MA0004.1;0.0714537,MA0006.1;0.232133,MA0007.1;0.0639049,MA0009.1;0.366503,MA0014.1;2.3917e-08,MA0017.1;0.125199,MA0019.1;0.145319,MA0024.1;0.285711,MA0025.1;0.47683,MA0027.1;1.89328,MA0028.1;1.13485,MA0029.1;0.30014,MA0030.1;0.291553,MA0031.1;0.24472,MA0038.1;0.120244,MA0040.1;0.304553,MA0041.1;0.0793669,MA0042.1;0.234471,MA0043.1;0.366755,MA0046.1;0.357837,MA0048.1;0.00292587,MA0050.1;0.066352,MA0051.1;0.118004,MA0052.1;0.307481,MA0055.1;0.019585,MA0056.1;0,MA0057.1;0.701911,MA0058.1;0.0375298,MA0059.1;0.340565,MA0060.1;0.0046941,MA0061.1;0.0176627,MA0063.1;0,MA0066.1;0.382686,MA0067.1;0.638784,MA0068.1;0.278942,MA0069.1;0.354782,MA0070.1;0.345954,MA0071.1;1.12049,MA0072.1;0.342425,MA0073.1;0.000371243,MA0074.1;0.375245,MA0076.1;0.16355,MA0077.1;0.336397,MA0078.1;0.175262,MA0081.1;0.0371987,MA0083.1;0.372513,MA0084.1;0.811454,MA0087.1;0.340509,MA0088.1;0.00200874,MA0089.1;0,MA0090.1;4.57128,MA0091.1;0.539562,MA0092.1;2.84647,MA0093.1;0.0219094,MA0095.1;0,MA0098.1;0,MA0100.1;0.127731,MA0101.1;0.0226238,MA0103.1;0.417468,MA0105.1;0.00755234,MA0106.1;0.14308,MA0107.1;0.00986632,MA0108.2;0.242565,MA0109.1;0,MA0111.1;0.192269,MA0113.1;0.152632,MA0114.1;0.0468005,MA0115.1;0.570409,MA0116.1;0.0103227,MA0117.1;0.396851,MA0119.1;0.569091,MA0122.1;0.418111,MA0124.1;0.533912,MA0125.1;0.461632,MA0130.1;0,MA0131.1;0.186723,MA0132.1;0,MA0133.1;0,MA0135.1;0.390959,MA0136.1;0.124027,MA0139.1;0.113636,MA0140.1;6.01712,MA0141.1;0.337366,MA0142.1;0.222682,MA0143.1;0.464654,MA0144.1;0.0075623,MA0145.1;0.0574606,MA0146.1;0.000172066,MA0147.1;0.0107968,MA0148.1;0.0821741,MA0149.1;0.647744,MA0062.2;0.00260174,MA0035.2;5.16386,MA0039.2;4.73092e-07,MA0138.2;0.176028,MA0002.2;0.157727,MA0137.2;0.0263382,MA0104.2;0.00463464,MA0047.2;0.136179,MA0112.2;0.00240105,MA0065.2;0.0287035,MA0150.1;0.0451191,MA0151.1;0,MA0152.1;1.66583,MA0153.1;0.447419,MA0154.1;0.00157043,MA0155.1;0.0812178,MA0156.1;0.0268872,MA0157.1;2.47306,MA0158.1;0,MA0159.1;0.146071,MA0160.1;0.0890912,MA0161.1;0,MA0162.1;2.37666e-07,MA0163.1;2.95855e-05,MA0164.1;0.160035,MA0080.2;0.095553,MA0018.2;0.143876,MA0099.2;0.102528,MA0079.2;1.58131e-07,MA0102.2;0.846442,MA0258.1;0.0065731,MA0259.1;0.313834,MA0442.1;0
}}
}}

Revision as of 19:04, 22 January 2013


Full id: C333_Fibroblast_Smooth_Preadipocyte_Adipocyte_Ewing_Placental_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr3:112317985..112318004,-p@chr3:112317985..112318004
-
Hg19::chr3:112318598..112318609,-p@chr3:112318598..112318609
-
Hg19::chr3:112320772..112320784,-p@chr3:112320772..112320784
-
Hg19::chr3:112324034..112324048,-p@chr3:112324034..112324048
-
Hg19::chr3:112356995..112357025,+p@chr3:112356995..112357025
+
Hg19::chr3:112357199..112357228,+p@chr3:112357199..112357228
+
Hg19::chr3:112357559..112357568,-p@chr3:112357559..112357568
-
Hg19::chr3:112357575..112357598,-p@chr3:112357575..112357598
-
Hg19::chr3:112357721..112357731,-p@chr3:112357721..112357731
-
Hg19::chr3:112357721..112357832,+p@chr3:112357721..112357832
+
Hg19::chr3:112357766..112357771,-p@chr3:112357766..112357771
-
Hg19::chr3:112357848..112357858,-p@chr3:112357848..112357858
-
Hg19::chr3:112358008..112358018,-p25@CCDC80
Hg19::chr3:112358055..112358066,-p24@CCDC80
Hg19::chr3:112358125..112358137,-p22@CCDC80
Hg19::chr3:112358228..112358239,-p31@CCDC80
Hg19::chr3:112358263..112358270,-p35@CCDC80
Hg19::chr3:112358632..112358646,-p5@CCDC80
Hg19::chr3:112359190..112359239,-p9@CCDC80
Hg19::chr3:112359295..112359306,-p19@CCDC80
Hg19::chr3:112359358..112359370,-p26@CCDC80
Hg19::chr3:112359375..112359386,-p27@CCDC80
Hg19::chr3:112359471..112359488,-p21@CCDC80
Hg19::chr3:112359502..112359520,-p13@CCDC80
Hg19::chr3:112359529..112359540,-p23@CCDC80
Hg19::chr3:112359550..112359569,-p7@CCDC80
Hg19::chr3:112359574..112359583,-p30@CCDC80
Hg19::chr3:112359611..112359633,-p18@CCDC80
Hg19::chr3:112359634..112359653,-p10@CCDC80
Hg19::chr3:112359654..112359671,-p15@CCDC80
Hg19::chr3:112359698..112359713,-p17@CCDC80
Hg19::chr3:112359729..112359753,+p@chr3:112359729..112359753
+
Hg19::chr3:112359880..112359894,-p2@CCDC80
Hg19::chr3:112359959..112359972,-p3@CCDC80
Hg19::chr3:112359975..112359997,-p1@CCDC80


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
muscle tissue9.65e-1764
musculature9.65e-1764
musculature of body9.65e-1764
skeletal muscle tissue3.61e-1662
striated muscle tissue3.61e-1662
myotome3.61e-1662
dense mesenchyme tissue6.69e-1573
somite8.45e-1571
presomitic mesoderm8.45e-1571
presumptive segmental plate8.45e-1571
dermomyotome8.45e-1571
trunk paraxial mesoderm8.45e-1571
paraxial mesoderm2.39e-1472
presumptive paraxial mesoderm2.39e-1472
multilaminar epithelium1.29e-1283
epithelial vesicle6.36e-1278
splanchnic layer of lateral plate mesoderm1.28e-1183
heart9.20e-1024
primitive heart tube9.20e-1024
primary heart field9.20e-1024
anterior lateral plate mesoderm9.20e-1024
heart tube9.20e-1024
heart primordium9.20e-1024
cardiac mesoderm9.20e-1024
cardiogenic plate9.20e-1024
heart rudiment9.20e-1024
mesoderm1.34e-09315
mesoderm-derived structure1.34e-09315
presumptive mesoderm1.34e-09315
mesenchyme2.94e-09160
entire embryonic mesenchyme2.94e-09160
trunk mesenchyme5.13e-09122
primary circulatory organ1.27e-0827
organ component layer2.26e-0766
omentum6.15e-076
peritoneum6.15e-076
abdominal cavity6.15e-076
visceral peritoneum6.15e-076
integument6.55e-0746
integumental system6.55e-0746
blood vessel layer6.62e-077
artery6.76e-0742
arterial blood vessel6.76e-0742
arterial system6.76e-0742
cardiovascular system7.93e-07109


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)
MA0003.14.93725e-10
MA0004.10.0714537
MA0006.10.232133
MA0007.10.0639049
MA0009.10.366503
MA0014.12.3917e-08
MA0017.10.125199
MA0019.10.145319
MA0024.10.285711
MA0025.10.47683
MA0027.11.89328
MA0028.11.13485
MA0029.10.30014
MA0030.10.291553
MA0031.10.24472
MA0038.10.120244
MA0040.10.304553
MA0041.10.0793669
MA0042.10.234471
MA0043.10.366755
MA0046.10.357837
MA0048.10.00292587
MA0050.10.066352
MA0051.10.118004
MA0052.10.307481
MA0055.10.019585
MA0056.10
MA0057.10.701911
MA0058.10.0375298
MA0059.10.340565
MA0060.10.0046941
MA0061.10.0176627
MA0063.10
MA0066.10.382686
MA0067.10.638784
MA0068.10.278942
MA0069.10.354782
MA0070.10.345954
MA0071.11.12049
MA0072.10.342425
MA0073.10.000371243
MA0074.10.375245
MA0076.10.16355
MA0077.10.336397
MA0078.10.175262
MA0081.10.0371987
MA0083.10.372513
MA0084.10.811454
MA0087.10.340509
MA0088.10.00200874
MA0089.10
MA0090.14.57128
MA0091.10.539562
MA0092.12.84647
MA0093.10.0219094
MA0095.10
MA0098.10
MA0100.10.127731
MA0101.10.0226238
MA0103.10.417468
MA0105.10.00755234
MA0106.10.14308
MA0107.10.00986632
MA0108.20.242565
MA0109.10
MA0111.10.192269
MA0113.10.152632
MA0114.10.0468005
MA0115.10.570409
MA0116.10.0103227
MA0117.10.396851
MA0119.10.569091
MA0122.10.418111
MA0124.10.533912
MA0125.10.461632
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.10.390959
MA0136.10.124027
MA0139.10.113636
MA0140.16.01712
MA0141.10.337366
MA0142.10.222682
MA0143.10.464654
MA0144.10.0075623
MA0145.10.0574606
MA0146.10.000172066
MA0147.10.0107968
MA0148.10.0821741
MA0149.10.647744
MA0062.20.00260174
MA0035.25.16386
MA0039.24.73092e-07
MA0138.20.176028
MA0002.20.157727
MA0137.20.0263382
MA0104.20.00463464
MA0047.20.136179
MA0112.20.00240105
MA0065.20.0287035
MA0150.10.0451191
MA0151.10
MA0152.11.66583
MA0153.10.447419
MA0154.10.00157043
MA0155.10.0812178
MA0156.10.0268872
MA0157.12.47306
MA0158.10
MA0159.10.146071
MA0160.10.0890912
MA0161.10
MA0162.12.37666e-07
MA0163.12.95855e-05
MA0164.10.160035
MA0080.20.095553
MA0018.20.143876
MA0099.20.102528
MA0079.21.58131e-07
MA0102.20.846442
MA0258.10.0065731
MA0259.10.313834
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
BCLAF1#977474.330529522024370.0009588178195446460.00689893036551314
EP300#2033112.128953113955860.009755139762610230.0366824023067347
MAFK#7975107.743066610808553.65307166813718e-071.80133688360991e-05
NR2C2#718287.45476820691228.71584813982768e-060.000235334659740296
POU2F2#545292.341574757705220.01145632032383210.0419113996882691
TRIM28#10155157.967367876541081.04717244445614e-101.13097872726531e-08



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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