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Coexpression cluster:C459: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.102469,0.000609221,0.0984893,1.04647,0.266493,0.545716,0.239567,0.544107,0.0294929,0.00531327,0.165709,0.272066,0.0182787,0.231159,1.41998,1.03468,0.416635,0.196076,0.0212388,0.0677633,1.63091,0.008045,0.180548,0.551194,0.392149,0.289541,0.343036,0.179098,0.0787487,0.299404,0.151697,0.448071,0.0406138,0.0187954,0.0614574,0.095179,0.0600845,0.186559,0.420263,0.0244783,0.0608563,0.141543,0.0373146,0.94426,8.32893e-05,0.115453,0.240368,0.158699,0.00127432,0.27085,0.300624,0.249086,0.0936711,0.515129,0.653159,0.233295,0.276619,0.209799,0.0544304,0.209089,0.483605,0.242112,0.122235,0.393294,0.255455,0.364726,0.73513,1.08739,0.43915,0.930562,0.133532,1.28082,0.00553467,0.651319,0.017273,0.0146455,0.157868,0.379205,0.436366,0.120546,0.240865,0.392395,0.709459,0.553244,0.604277,0.000162154,0.02106,0.0102959,0.321213,1.18432,0.823081,0.579812,0.462581,0.0432003,0.267495,0.717807,0.0208754,0.499768,0.324895,0.00795051,0.423302,0.45769,0.494867,0.419744,0.355282,0.16277,0.406348,0.228655,0.123981,0.0697646,0.69516,0.492438,0.316828,0.171884,0.777703,0.215264,0.000295464,0.15094,0.362802,0.0442476,0.64371,0.319278,0.183912,0.263675,0.882719,0.379837,0.662381,0.466912,0.683004,0.408938,0.580435,0.466574,0.696335,0.26116,0.835304,0.0469425,1.42521,0.179476,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.356718,0.20386,0.343142,1.4753,0.139503,0.0420132,0.0255653,0.00135206,0.58078,0.113903,0.678325,0.959994,0.308372,0.0706846,0.124164,0.107739,0.758809,0.564094,0.435692,0.109525,1.72095,0.254599,0.0377709,0.238589,1.27886e-06
|tfbs_overrepresentation_jaspar=MA0003.1;8.95462e-07,MA0004.1;0.505176,MA0006.1;0.0763783,MA0007.1;0.156885,MA0009.1;0.543169,MA0014.1;1.91579e-05,MA0017.1;0.0964051,MA0019.1;0.275941,MA0024.1;0.450307,MA0025.1;0.665335,MA0027.1;2.11401,MA0028.1;0.0843345,MA0029.1;0.467171,MA0030.1;2.01824,MA0031.1;1.82996,MA0038.1;0.24162,MA0040.1;1.19016,MA0041.1;2.30795,MA0042.1;0.938412,MA0043.1;0.543454,MA0046.1;0.533373,MA0048.1;0.00619675,MA0050.1;0.940798,MA0051.1;0.238478,MA0052.1;0.475699,MA0055.1;0.00257143,MA0056.1;0,MA0057.1;0.00555109,MA0058.1;0.35609,MA0059.1;0.109562,MA0060.1;0.0296044,MA0061.1;0.0219462,MA0063.1;0,MA0066.1;0.241938,MA0067.1;0.83875,MA0068.1;0.0636439,MA0069.1;0.529912,MA0070.1;0.519883,MA0071.1;0.213282,MA0072.1;0.515863,MA0073.1;9.85772e-11,MA0074.1;0.23792,MA0076.1;0.119431,MA0077.1;2.19066,MA0078.1;0.31524,MA0081.1;0.718628,MA0083.1;0.549943,MA0084.1;1.01907,MA0087.1;1.27862,MA0088.1;0.0366926,MA0089.1;0,MA0090.1;0.127987,MA0091.1;0.509438,MA0092.1;0.146372,MA0093.1;0.566557,MA0095.1;0,MA0098.1;0,MA0100.1;0.252028,MA0101.1;0.0794742,MA0103.1;0.0719484,MA0105.1;0.00427625,MA0106.1;0.272934,MA0107.1;0.046982,MA0108.2;1.82106,MA0109.1;0,MA0111.1;0.136202,MA0113.1;0.285689,MA0114.1;0.17185,MA0115.1;0.766188,MA0116.1;0.40798,MA0117.1;0.577217,MA0119.1;0.100647,MA0122.1;0.600851,MA0124.1;1.7262,MA0125.1;0.648747,MA0130.1;0,MA0131.1;0.329895,MA0132.1;0,MA0133.1;0,MA0135.1;1.39934,MA0136.1;0.690268,MA0139.1;0.018888,MA0140.1;0.211376,MA0141.1;0.108582,MA0142.1;0.374765,MA0143.1;0.285827,MA0144.1;0.0397909,MA0145.1;0.00212809,MA0146.1;1.04313e-05,MA0147.1;0.049714,MA0148.1;1.64717,MA0149.1;0.204488,MA0062.2;0.0205944,MA0035.2;0.210872,MA0039.2;1.45259e-05,MA0138.2;0.316226,MA0002.2;0.499059,MA0137.2;0.0876366,MA0104.2;0.0293723,MA0047.2;1.34068,MA0112.2;0.0117779,MA0065.2;0.220145,MA0150.1;0.393024,MA0151.1;0,MA0152.1;2.55659,MA0153.1;0.633172,MA0154.1;0.00405158,MA0155.1;0.0886229,MA0156.1;1.03924,MA0157.1;1.65846,MA0158.1;0,MA0159.1;0.049967,MA0160.1;0.196462,MA0161.1;0,MA0162.1;7.59857e-05,MA0163.1;0.00138779,MA0164.1;2.22695,MA0080.2;0.566769,MA0018.2;0.274004,MA0099.2;0.216352,MA0079.2;0,MA0102.2;1.05522,MA0258.1;0.0364681,MA0259.1;0.0531061,MA0442.1;0
}}
}}

Revision as of 19:11, 22 January 2013


Full id: C459_diffuse_acute_testicular_iPS_CD14_Renal_chronic



Phase1 CAGE Peaks

Hg19::chr10:112360803..112360817,+p@chr10:112360803..112360817
+
Hg19::chr10:70098368..70098404,+p3@HNRNPH3
Hg19::chr1:245019788..245019803,-p@chr1:245019788..245019803
-
Hg19::chr1:245022599..245022657,-p7@HNRNPU
Hg19::chr1:44588180..44588202,-p1@ENST00000402743
Hg19::chr6:114267231..114267258,-p@chr6:114267231..114267258
-
Hg19::chr7:26233209..26233239,-p@chr7:26233209..26233239
-
Hg19::chr7:26233242..26233284,-p@chr7:26233242..26233284
-
Hg19::chr7:26233292..26233320,-p@chr7:26233292..26233320
-
Hg19::chr7:26235486..26235540,-p@chr7:26235486..26235540
-
Hg19::chr7:26236054..26236075,-p@chr7:26236054..26236075
-
Hg19::chr7:26236076..26236108,-p@chr7:26236076..26236108
-
Hg19::chr7:26236464..26236483,-p3@HNRNPA2B1
Hg19::chr7:26236559..26236570,-p9@HNRNPA2B1
Hg19::chr7:26236592..26236600,-p11@HNRNPA2B1
Hg19::chr7:26236610..26236626,-p5@HNRNPA2B1
Hg19::chr7:26236630..26236642,-p8@HNRNPA2B1
Hg19::chr7:26236955..26236980,-p6@HNRNPA2B1
Hg19::chr7:26236987..26237030,-p4@HNRNPA2B1
Hg19::chr7:26237039..26237051,-p@chr7:26237039..26237051
-
Hg19::chr7:26237272..26237323,-p@chr7:26237272..26237323
-


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

p.valueFDRnGenesnPathwayName
6.54125989539596e-050.02526476491379392134mRNA processing (Wikipathways):WP1863
7.98254815601705e-050.02526476491379392148mRNA Processing (Reactome):REACT_1675
0.000137231274343340.02895579888644482194{POLR2A,195} (Static Module):NA



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:0030530heterogeneous nuclear ribonucleoprotein complex1.45832616951182e-05
GO:0005681spliceosome0.000457085172934245
GO:0008380RNA splicing0.000800649661692765
GO:0006397mRNA processing0.000884717876170506
GO:0016071mRNA metabolic process0.00111158767673731
GO:0043047single-stranded telomeric DNA binding0.00187294831574558
GO:0006396RNA processing0.00187294831574558
GO:0003723RNA binding0.00539548910907402
GO:0042162telomeric DNA binding0.00539548910907402
GO:0044428nuclear part0.00560587338291255
GO:0030529ribonucleoprotein complex0.00560587338291255
GO:0003697single-stranded DNA binding0.0150951373577981
GO:0000375RNA splicing, via transesterification reactions0.0150951373577981
GO:0000398nuclear mRNA splicing, via spliceosome0.0150951373577981
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0150951373577981
GO:0050658RNA transport0.0156575469235196
GO:0051236establishment of RNA localization0.0156575469235196
GO:0050657nucleic acid transport0.0156575469235196
GO:0006403RNA localization0.0156575469235196
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0168118700284401
GO:0009986cell surface0.0227705399221662
GO:0043566structure-specific DNA binding0.0233472040861499
GO:0003677DNA binding0.0254627520372707
GO:0032991macromolecular complex0.0299326331208392
GO:0044446intracellular organelle part0.0304654080166691
GO:0044422organelle part0.0304654080166691
GO:0016070RNA metabolic process0.0304654080166691
GO:0000166nucleotide binding0.0309391045519627
GO:0010467gene expression0.0488748993612867



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><br>disease_data<br>

Disease
Ontology termp-valuen
disease of cellular proliferation1.02e-24239
cancer1.43e-24235
cell type cancer7.61e-12143
hematologic cancer8.91e-1151
immune system cancer8.91e-1151
organ system cancer2.02e-09137
carcinoma2.64e-09106
leukemia1.92e-0839


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)
MA0003.18.95462e-07
MA0004.10.505176
MA0006.10.0763783
MA0007.10.156885
MA0009.10.543169
MA0014.11.91579e-05
MA0017.10.0964051
MA0019.10.275941
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.12.01824
MA0031.11.82996
MA0038.10.24162
MA0040.11.19016
MA0041.12.30795
MA0042.10.938412
MA0043.10.543454
MA0046.10.533373
MA0048.10.00619675
MA0050.10.940798
MA0051.10.238478
MA0052.10.475699
MA0055.10.00257143
MA0056.10
MA0057.10.00555109
MA0058.10.35609
MA0059.10.109562
MA0060.10.0296044
MA0061.10.0219462
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.10.0636439
MA0069.10.529912
MA0070.10.519883
MA0071.10.213282
MA0072.10.515863
MA0073.19.85772e-11
MA0074.10.23792
MA0076.10.119431
MA0077.12.19066
MA0078.10.31524
MA0081.10.718628
MA0083.10.549943
MA0084.11.01907
MA0087.11.27862
MA0088.10.0366926
MA0089.10
MA0090.10.127987
MA0091.10.509438
MA0092.10.146372
MA0093.10.566557
MA0095.10
MA0098.10
MA0100.10.252028
MA0101.10.0794742
MA0103.10.0719484
MA0105.10.00427625
MA0106.10.272934
MA0107.10.046982
MA0108.21.82106
MA0109.10
MA0111.10.136202
MA0113.10.285689
MA0114.10.17185
MA0115.10.766188
MA0116.10.40798
MA0117.10.577217
MA0119.10.100647
MA0122.10.600851
MA0124.11.7262
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.11.39934
MA0136.10.690268
MA0139.10.018888
MA0140.10.211376
MA0141.10.108582
MA0142.10.374765
MA0143.10.285827
MA0144.10.0397909
MA0145.10.00212809
MA0146.11.04313e-05
MA0147.10.049714
MA0148.11.64717
MA0149.10.204488
MA0062.20.0205944
MA0035.20.210872
MA0039.21.45259e-05
MA0138.20.316226
MA0002.20.499059
MA0137.20.0876366
MA0104.20.0293723
MA0047.21.34068
MA0112.20.0117779
MA0065.20.220145
MA0150.10.393024
MA0151.10
MA0152.12.55659
MA0153.10.633172
MA0154.10.00405158
MA0155.10.0886229
MA0156.11.03924
MA0157.11.65846
MA0158.10
MA0159.10.049967
MA0160.10.196462
MA0161.10
MA0162.17.59857e-05
MA0163.10.00138779
MA0164.12.22695
MA0080.20.566769
MA0018.20.274004
MA0099.20.216352
MA0079.20
MA0102.21.05522
MA0258.10.0364681
MA0259.10.0531061
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
BCL3#60246.580400534045390.002828160208479960.015476564003848



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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