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Coexpression cluster:C811: Difference between revisions

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{{Coexpression_clusters
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reticulum lumen!4.61097154483163e-05!55033;51661;813$GO:0044432!endoplasmic reticulum part!0.000235163406472688!55033;51661;81555;813$GO:0005783!endoplasmic reticulum!0.00139924532238113!55033;51661;81555;813$GO:0003755!peptidyl-prolyl cis-trans isomerase activity!0.00533970528070001!55033;51661$GO:0016859!cis-trans isomerase activity!0.00533970528070001!55033;51661$GO:0016051!carbohydrate biosynthetic process!0.00978051326245874!83468;55830$GO:0005588!collagen type V!0.013117345110061!1290$GO:0031974!membrane-enclosed lumen!0.0169083956011319!55033;51661;813$GO:0043233!organelle lumen!0.0169083956011319!55033;51661;813$GO:0043588!skin development!0.0183586078254092!1290$GO:0016758!transferase activity, transferring hexosyl groups!0.0218303482719949!83468;55830$GO:0016853!isomerase activity!0.0235269792804304!55033;51661$GO:0030199!collagen fibril organization!0.0235269792804304!1290$GO:0005583!fibrillar collagen!0.0239659625334093!1290$GO:0006457!protein folding!0.0239659625334093!55033;51661$GO:0005509!calcium ion binding!0.0305126129548744!55033;51661;813$GO:0031410!cytoplasmic vesicle!0.0308570937043425!81555;813$GO:0031982!vesicle!0.0308570937043425!81555;813$GO:0016757!transferase activity, transferring glycosyl 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|full_id=C811_Smooth_Fibroblast_Preadipocyte_Chondrocyte_hepatic_basal_Adipocyte
|id=C811
}}

Latest revision as of 11:31, 17 September 2013


Full id: C811_Smooth_Fibroblast_Preadipocyte_Chondrocyte_hepatic_basal_Adipocyte



Phase1 CAGE Peaks

Hg19::chr12:104443890..104443971,-p1@GLT8D2
Hg19::chr12:99038511..99038575,-p1@IKBIP
Hg19::chr1:162602244..162602289,+p1@DDR2
Hg19::chr2:179343268..179343338,-p1@FKBP7
Hg19::chr2:190044480..190044494,-p1@COL5A2
Hg19::chr3:52739588..52739621,-p2@GLT8D1
Hg19::chr5:143550159..143550236,-p1@YIPF5
Hg19::chr5:54455989..54456019,+p1@GPX8
Hg19::chr7:128379390..128379447,+p1@CALU
Hg19::chr7:30066233..30066332,-p1@FKBP14


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:0005788endoplasmic reticulum lumen4.61097154483163e-05
GO:0044432endoplasmic reticulum part0.000235163406472688
GO:0005783endoplasmic reticulum0.00139924532238113
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.00533970528070001
GO:0016859cis-trans isomerase activity0.00533970528070001
GO:0016051carbohydrate biosynthetic process0.00978051326245874
GO:0005588collagen type V0.013117345110061
GO:0031974membrane-enclosed lumen0.0169083956011319
GO:0043233organelle lumen0.0169083956011319
GO:0043588skin development0.0183586078254092
GO:0016758transferase activity, transferring hexosyl groups0.0218303482719949
GO:0016853isomerase activity0.0235269792804304
GO:0030199collagen fibril organization0.0235269792804304
GO:0005583fibrillar collagen0.0239659625334093
GO:0006457protein folding0.0239659625334093
GO:0005509calcium ion binding0.0305126129548744
GO:0031410cytoplasmic vesicle0.0308570937043425
GO:0031982vesicle0.0308570937043425
GO:0016757transferase activity, transferring glycosyl groups0.0308570937043425



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
dense mesenchyme tissue4.01e-2073
somite5.00e-2071
presomitic mesoderm5.00e-2071
presumptive segmental plate5.00e-2071
dermomyotome5.00e-2071
trunk paraxial mesoderm5.00e-2071
paraxial mesoderm1.61e-1972
presumptive paraxial mesoderm1.61e-1972
multilaminar epithelium2.34e-1983
skeletal muscle tissue4.90e-1862
striated muscle tissue4.90e-1862
myotome4.90e-1862
muscle tissue1.40e-1764
musculature1.40e-1764
musculature of body1.40e-1764
epithelial vesicle1.44e-1678
unilaminar epithelium3.18e-15148
splanchnic layer of lateral plate mesoderm2.09e-1483
mesenchyme3.17e-14160
entire embryonic mesenchyme3.17e-14160
trunk mesenchyme7.25e-14122
surface structure1.03e-1399
vasculature2.43e-1378
vascular system2.43e-1378
organism subdivision6.66e-13264
artery2.83e-1142
arterial blood vessel2.83e-1142
arterial system2.83e-1142
integument3.71e-1146
integumental system3.71e-1146
epithelial tube open at both ends3.81e-1159
blood vessel3.81e-1159
blood vasculature3.81e-1159
vascular cord3.81e-1159
vessel8.74e-1168
multi-cellular organism2.36e-10656
trunk3.57e-10199
systemic artery3.83e-1033
systemic arterial system3.83e-1033
skin of body9.29e-1041
multi-tissue structure4.07e-09342
cardiovascular system7.21e-09109
circulatory system9.15e-09112
epithelial tube3.08e-08117
organ component layer4.11e-0866
anatomical system5.74e-08624
anatomical group7.50e-08625
cell layer7.93e-08309
epithelium2.16e-07306
anatomical cluster7.32e-07373


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)
MA0003.10.456919
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.686562
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
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.963243
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.11.19169
MA0052.10.753928
MA0055.10.014035
MA0056.10
MA0057.10.46253
MA0058.10.293055
MA0059.10.291897
MA0060.11.37052
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.11.88295
MA0071.10.440254
MA0072.10.798564
MA0073.10.0824235
MA0074.10.4723
MA0076.11.50024
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.11.2287
MA0101.10.241637
MA0103.10.228129
MA0105.10.741916
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.11.1801
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.14293
MA0146.10.0169564
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.740103
MA0035.20.437071
MA0039.20.360905
MA0138.20.569505
MA0002.20.407187
MA0137.20.710884
MA0104.20.138396
MA0047.20.504873
MA0112.20.313961
MA0065.20.0371828
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.296882
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.229496
MA0163.10.0235237
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.20.227142
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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
CCNT2#90553.168100788481320.01227157669794290.0444810050587048
CEBPB#105164.782688575494890.0005200755356730160.00450569629781453
GTF2B#295939.583148980297270.00311863167294360.0163910610080296
IRF1#365953.818581876781950.005465628575453730.0247571142295968
MXI1#460143.984628651503720.01296562982531040.0460130284184168
POLR2A#5430102.147453176558070.0004793377491637920.00436532570499802
SIN3A#2594263.245330836089080.004223840630485730.0201027019507519
TAF1#687282.674437028596230.001556617278062390.00988457177014395
TBP#690872.594739480967470.00558866901773640.0252738808150763
TRIM28#1015535.577157513578760.01403197805233580.0492484375376517



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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