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Coexpression cluster:C463: Difference between revisions

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{{Coexpression_clusters
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process!0.00688389882661927!54361;10631;131118;5588;10290$GO:0048856!anatomical structure development!0.0111239349841107!10631;131118;5588;10290$GO:0007275!multicellular organismal development!0.0126389772157664!54361;10631;131118;10290$GO:0008285!negative regulation of cell proliferation!0.0189097449991574!5918;10290$GO:0048513!organ development!0.0189097449991574!10631;131118;10290$GO:0048731!system development!0.0285564188245063!10631;131118;10290$GO:0032501!multicellular organismal process!0.0285564188245063!54361;10631;131118;10290$GO:0048806!genitalia development!0.0285564188245063!131118$GO:0005578!proteinaceous extracellular matrix!0.0285564188245063!54361;10631$GO:0043681!protein import into mitochondrion!0.0285564188245063!131118$GO:0004697!protein kinase C activity!0.0285564188245063!5588$GO:0001565!phorbol ester receptor activity!0.0285564188245063!5588$GO:0042127!regulation of cell 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63528,0.545716,1.25081,0.295736,0.536019,0.337519,0.496783,0.748251,1.35703,0.231159,0.264653,0.0881735,0.416635,0.434454,0.0930871,0.153235,0.324802,0.835453,0.533052,0.259643,0.124129,0.289541,0.173284,0.179098,0.965823,0.147924,0.462061,1.13801,0.362042,0.21322,0.831295,0.0501616,0.0600845,0.547612,0.738471,1.53913,0.21951,0.141543,0.0917928,0.262615,0.314233,0.744956,0.240368,0.158699,0.159934,0.078811,0.300624,0.249086,0.20228,0.515129,0.653159,0.233295,0.581687,0.603257,0.299101,0.209089,0.483605,0.679156,0.122235,0.393294,0.71007,0.364726,0.73513,1.08739,0.43915,0.930562,0.416257,0.130122,0.197136,0.651319,0.201153,0.353555,0.316622,0.379205,0.436366,0.120546,0.240865,1.01704,0.25519,1.70833,0.604277,1.50696,0.02106,0.140525,0.321213,1.18432,0.823081,0.579812,0.462581,0.0432003,0.0776122,1.55902,0.710498,0.499768,0.324895,0.24534,0.743127,0.45769,0.494867,0.419744,0.935363,0.48954,0.406348,0.228655,0.391767,0.897424,0.104554,0.492438,0.0955593,0.171884,0.777703,0.215264,1.16925,0.15094,0.362802,0.383976,0.64371,0.319278,0.541208,0.263675,0.882719,0.379837,1.91516,0.466912,0.683004,0.182525,0.580435,0.466574,0.696335,0.723221,0.835304,0.268768,0.147939,0.179476,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.356718,0.589128,0.343142,1.4753,0.139503,0.370558,0.507246,0.446854,0.58078,0.81624,0.678325,0.959994,0.308372,0.247915,0.124164,0.107739,0.758809,0.564094,1.11126,0.109525,0.36994,0.708093,0.344454,1.24712,1.44474|tfbs_overrepresentation_jaspar=MA0003.1;0.477238,MA0004.1;0.169125,MA0006.1;0.0763783,MA0007.1;0.156885,MA0009.1;0.543169,MA0014.1;1.30323,MA0017.1;0.657001,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;0.457153,MA0031.1;0.401568,MA0038.1;1.25856,MA0040.1;0.472301,MA0041.1;0.181587,MA0042.1;0.483482,MA0043.1;2.30395,MA0046.1;0.533373,MA0048.1;0.375507,MA0050.1;0.160894,MA0051.1;0.238478,MA0052.1;0.475699,MA0055.1;0.710409,MA0056.1;0,MA0057.1;0.354274,MA0058.1;0.110291,MA0059.1;0.109562,MA0060.1;0.0296044,MA0061.1;1.46814,MA0063.1;0,MA0066.1;0.241938,MA0067.1;0.83875,MA0068.1;0.334888,MA0069.1;0.529912,MA0070.1;0.519883,MA0071.1;0.213282,MA0072.1;0.515863,MA0073.1;0.336217,MA0074.1;0.23792,MA0076.1;0.119431,MA0077.1;1.26861,MA0078.1;2.32537,MA0081.1;0.109654,MA0083.1;0.549943,MA0084.1;1.01907,MA0087.1;0.513678,MA0088.1;0.307877,MA0089.1;0,MA0090.1;0.402075,MA0091.1;0.509438,MA0092.1;0.146372,MA0093.1;0.0778562,MA0095.1;0,MA0098.1;0,MA0100.1;0.702151,MA0101.1;0.272702,MA0103.1;0.251512,MA0105.1;0.731971,MA0106.1;0.272934,MA0107.1;0.177872,MA0108.2;1.03141,MA0109.1;0,MA0111.1;0.136202,MA0113.1;0.779331,MA0114.1;0.17185,MA0115.1;0.766188,MA0116.1;1.5622,MA0117.1;1.41321,MA0119.1;0.676972,MA0122.1;0.600851,MA0124.1;0.727093,MA0125.1;0.648747,MA0130.1;0,MA0131.1;0.329895,MA0132.1;0,MA0133.1;0,MA0135.1;0.570637,MA0136.1;0.246897,MA0139.1;1.37627,MA0140.1;0.606998,MA0141.1;0.108582,MA0142.1;0.374765,MA0143.1;1.42229,MA0144.1;0.356992,MA0145.1;0.356381,MA0146.1;1.35977,MA0147.1;0.186237,MA0148.1;0.185927,MA0149.1;0.204488,MA0062.2;0.0205944,MA0035.2;0.605801,MA0039.2;0.126459,MA0138.2;0.316226,MA0002.2;1.16349,MA0137.2;0.614924,MA0104.2;0.121334,MA0047.2;0.263601,MA0112.2;0.979121,MA0065.2;1.06701,MA0150.1;0.393024,MA0151.1;0,MA0152.1;0.216094,MA0153.1;0.633172,MA0154.1;1.30847,MA0155.1;0.303035,MA0156.1;0.0888107,MA0157.1;0.352016,MA0158.1;0,MA0159.1;0.049967,MA0160.1;0.571442,MA0161.1;0,MA0162.1;0.595981,MA0163.1;1.62931,MA0164.1;0.295453,MA0080.2;0.268297,MA0018.2;0.274004,MA0099.2;0.216352,MA0079.2;0.144307,MA0102.2;2.39833,MA0258.1;0.953225,MA0259.1;0.0531061,MA0442.1;0}}
|full_id=C463_Mesothelial_mesothelioma_Sertoli_mesenchymal_vagina_Cardiac_Fibroblast
|id=C463
}}

Latest revision as of 11:23, 17 September 2013


Full id: C463_Mesothelial_mesothelioma_Sertoli_mesenchymal_vagina_Cardiac_Fibroblast



Phase1 CAGE Peaks

Hg19::chr10:6622278..6622290,-p6@PRKCQ
Hg19::chr11:116728907..116728948,+p2@CU690121
Hg19::chr13:38091764..38091775,+p@chr13:38091764..38091775
+
Hg19::chr13:38145825..38145840,-p14@POSTN
Hg19::chr13:38148733..38148753,-p@chr13:38148733..38148753
-
Hg19::chr13:97328912..97328917,+p@chr13:97328912..97328917
+
Hg19::chr1:22469560..22469567,-p3@WNT4
Hg19::chr20:6033732..6033760,-p8@AB527789
Hg19::chr20:6034216..6034224,-p@chr20:6034216..6034224
-
Hg19::chr20:6034506..6034518,-p4@LRRN4
Hg19::chr20:61687988..61688007,-p@chr20:61687988..61688007
-
Hg19::chr20:8101412..8101426,+p@chr20:8101412..8101426
+
Hg19::chr20:8101451..8101452,+p@chr20:8101451..8101452
+
Hg19::chr2:10454550..10454555,+p@chr2:10454550..10454555
+
Hg19::chr2:220309299..220309306,+p32@SPEG
Hg19::chr3:158450428..158450431,-p9@RARRES1
Hg19::chr3:158450447..158450473,-p4@RARRES1
Hg19::chr3:158450475..158450494,-p6@RARRES1
Hg19::chr3:180707620..180707631,-p3@DNAJC19
Hg19::chr4:146267392..146267393,-p@chr4:146267392..146267393
-
Hg19::chr8:140663726..140663732,-p@chr8:140663726..140663732
-


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:0032502developmental process0.00688389882661927
GO:0048856anatomical structure development0.0111239349841107
GO:0007275multicellular organismal development0.0126389772157664
GO:0008285negative regulation of cell proliferation0.0189097449991574
GO:0048513organ development0.0189097449991574
GO:0048731system development0.0285564188245063
GO:0032501multicellular organismal process0.0285564188245063
GO:0048806genitalia development0.0285564188245063
GO:0005578proteinaceous extracellular matrix0.0285564188245063
GO:0043681protein import into mitochondrion0.0285564188245063
GO:0004697protein kinase C activity0.0285564188245063
GO:0001565phorbol ester receptor activity0.0285564188245063
GO:0042127regulation of cell proliferation0.0285564188245063



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>

Cell Type
Ontology termp-valuen
mesothelial cell1.94e-1619
Uber Anatomy
Ontology termp-valuen
right ovary7.49e-085
Disease
Ontology termp-valuen
ovarian cancer7.70e-2214
female reproductive organ cancer9.99e-1227
reproductive organ cancer5.69e-1129


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)
MA0003.10.477238
MA0004.10.169125
MA0006.10.0763783
MA0007.10.156885
MA0009.10.543169
MA0014.11.30323
MA0017.10.657001
MA0019.10.275941
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.0843345
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.11.25856
MA0040.10.472301
MA0041.10.181587
MA0042.10.483482
MA0043.12.30395
MA0046.10.533373
MA0048.10.375507
MA0050.10.160894
MA0051.10.238478
MA0052.10.475699
MA0055.10.710409
MA0056.10
MA0057.10.354274
MA0058.10.110291
MA0059.10.109562
MA0060.10.0296044
MA0061.11.46814
MA0063.10
MA0066.10.241938
MA0067.10.83875
MA0068.10.334888
MA0069.10.529912
MA0070.10.519883
MA0071.10.213282
MA0072.10.515863
MA0073.10.336217
MA0074.10.23792
MA0076.10.119431
MA0077.11.26861
MA0078.12.32537
MA0081.10.109654
MA0083.10.549943
MA0084.11.01907
MA0087.10.513678
MA0088.10.307877
MA0089.10
MA0090.10.402075
MA0091.10.509438
MA0092.10.146372
MA0093.10.0778562
MA0095.10
MA0098.10
MA0100.10.702151
MA0101.10.272702
MA0103.10.251512
MA0105.10.731971
MA0106.10.272934
MA0107.10.177872
MA0108.21.03141
MA0109.10
MA0111.10.136202
MA0113.10.779331
MA0114.10.17185
MA0115.10.766188
MA0116.11.5622
MA0117.11.41321
MA0119.10.676972
MA0122.10.600851
MA0124.10.727093
MA0125.10.648747
MA0130.10
MA0131.10.329895
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.11.37627
MA0140.10.606998
MA0141.10.108582
MA0142.10.374765
MA0143.11.42229
MA0144.10.356992
MA0145.10.356381
MA0146.11.35977
MA0147.10.186237
MA0148.10.185927
MA0149.10.204488
MA0062.20.0205944
MA0035.20.605801
MA0039.20.126459
MA0138.20.316226
MA0002.21.16349
MA0137.20.614924
MA0104.20.121334
MA0047.20.263601
MA0112.20.979121
MA0065.21.06701
MA0150.10.393024
MA0151.10
MA0152.10.216094
MA0153.10.633172
MA0154.11.30847
MA0155.10.303035
MA0156.10.0888107
MA0157.10.352016
MA0158.10
MA0159.10.049967
MA0160.10.571442
MA0161.10
MA0162.10.595981
MA0163.11.62931
MA0164.10.295453
MA0080.20.268297
MA0018.20.274004
MA0099.20.216352
MA0079.20.144307
MA0102.22.39833
MA0258.10.953225
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

No analysis results for this cluster

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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