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{{Coexpression_clusters
{
|full_id=C331_kidney_thyroid_breast_Adipocyte_adipose_retina_vagina
|

Latest revision as of 11:20, 17 September 2013


Full id: C331_kidney_thyroid_breast_Adipocyte_adipose_retina_vagina



Phase1 CAGE Peaks

Hg19::chr11:60836185..60836188,-p@chr11:60836185..60836188
-
Hg19::chr14:104715586..104715589,+p@chr14:104715586..104715589
+
Hg19::chr5:150400145..150400158,+p1@GPX3
Hg19::chr5:150404893..150404902,+p4@GPX3
Hg19::chr5:150404904..150404928,+p@chr5:150404904..150404928
+
Hg19::chr5:150404932..150404941,+p@chr5:150404932..150404941
+
Hg19::chr5:150404956..150404977,+p@chr5:150404956..150404977
+
Hg19::chr5:150404964..150404982,-p@chr5:150404964..150404982
-
Hg19::chr5:150404991..150405006,+p@chr5:150404991..150405006
+
Hg19::chr5:150406455..150406487,+p3@GPX3
Hg19::chr5:150406486..150406500,-p@chr5:150406486..150406500
-
Hg19::chr5:150406528..150406537,+p@chr5:150406528..150406537
+
Hg19::chr5:150406539..150406588,-p@chr5:150406539..150406588
-
Hg19::chr5:150406546..150406555,+p@chr5:150406546..150406555
+
Hg19::chr5:150407007..150407019,+p@chr5:150407007..150407019
+
Hg19::chr5:150407015..150407023,-p@chr5:150407015..150407023
-
Hg19::chr5:150407045..150407060,+p@chr5:150407045..150407060
+
Hg19::chr5:150407573..150407582,+p@chr5:150407573..150407582
+
Hg19::chr5:150407683..150407708,-p4@CU690655
Hg19::chr5:150407695..150407704,+p@chr5:150407695..150407704
+
Hg19::chr5:150407726..150407744,-p3@CU690655
Hg19::chr5:150407728..150407739,+p@chr5:150407728..150407739
+
Hg19::chr5:150407741..150407750,+p@chr5:150407741..150407750
+
Hg19::chr5:150407760..150407799,-p1@CU690655
Hg19::chr5:150407800..150407825,-p2@CU690655
Hg19::chr5:150407829..150407840,+p@chr5:150407829..150407840
+
Hg19::chr5:150407857..150407891,+p@chr5:150407857..150407891
+
Hg19::chr5:150407894..150407949,+p@chr5:150407894..150407949
+
Hg19::chr5:150407957..150408028,+p@chr5:150407957..150408028
+
Hg19::chr5:150408069..150408081,+p@chr5:150408069..150408081
+
Hg19::chr5:150408124..150408137,+p@chr5:150408124..150408137
+
Hg19::chr5:150408168..150408181,-p5@CU690655
Hg19::chr5:150408185..150408218,+p@chr5:150408185..150408218
+
Hg19::chr5:150408223..150408268,-p@chr5:150408223..150408268
-
Hg19::chr5:150408230..150408259,+p@chr5:150408230..150408259
+


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:0006982response to lipid hydroperoxide0.00123631225715295
GO:0033194response to hydroperoxide0.00123631225715295
GO:0043295glutathione binding0.00123631225715295
GO:0051289protein homotetramerization0.0024726245143059
GO:0042744hydrogen peroxide catabolic process0.0024726245143059
GO:0042743hydrogen peroxide metabolic process0.0024726245143059
GO:0004602glutathione peroxidase activity0.0024726245143059
GO:0051262protein tetramerization0.0024726245143059
GO:0006749glutathione metabolic process0.0024726245143059
GO:0042542response to hydrogen peroxide0.0024726245143059
GO:0000302response to reactive oxygen species0.0030345846311936
GO:0051260protein homooligomerization0.00422406687860591
GO:0006800oxygen and reactive oxygen species metabolic process0.00427954242860636
GO:0008430selenium binding0.00441540091840339
GO:0051259protein oligomerization0.00487252477819103
GO:0004601peroxidase activity0.00487252477819103
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.00487252477819103
GO:0006790sulfur metabolic process0.00590682522861964
GO:0006979response to oxidative stress0.00780828793991336
GO:0042277peptide binding0.0128576474743907
GO:0005625soluble fraction0.0137760508654186
GO:0006732coenzyme metabolic process0.0161844513663659
GO:0006461protein complex assembly0.0176689626751442
GO:0051186cofactor metabolic process0.0176689626751442
GO:0008134transcription factor binding0.021363475803603
GO:0005615extracellular space0.0251066489144907
GO:0042221response to chemical stimulus0.0269699229430773
GO:0065003macromolecular complex assembly0.0333804309431296
GO:0044248cellular catabolic process0.0335040621688449
GO:0022607cellular component assembly0.0335040621688449
GO:0000267cell fraction0.035157629812787
GO:0044421extracellular region part0.035157629812787
GO:0009056catabolic process0.0364524795821157
GO:0006950response to stress0.0444345170070854



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>

Cell Type
Ontology termp-valuen
fat cell1.99e-1215
respiratory epithelial cell1.42e-0813
Uber Anatomy
Ontology termp-valuen
adult organism1.11e-33114
subdivision of digestive tract1.73e-07118
organ1.96e-07503
subdivision of trunk3.87e-07112
endoderm-derived structure4.08e-07160
endoderm4.08e-07160
presumptive endoderm4.08e-07160


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)
MA0003.10.000577223
MA0004.12.48023
MA0006.10.441316
MA0007.10.0639049
MA0009.10.366503
MA0014.10.000100173
MA0017.10.0305232
MA0019.10.145319
MA0024.10.285711
MA0025.10.47683
MA0027.11.89328
MA0028.10.105723
MA0029.10.30014
MA0030.10.291553
MA0031.11.96692
MA0038.10.120244
MA0040.10.304553
MA0041.10.0793669
MA0042.10.065999
MA0043.10.366755
MA0046.10.357837
MA0048.10.078067
MA0050.10.066352
MA0051.10.118004
MA0052.10.307481
MA0055.10.019585
MA0056.10
MA0057.10.13475
MA0058.16.39417
MA0059.14.89766
MA0060.10.0808803
MA0061.10.0571069
MA0063.10
MA0066.11.25373
MA0067.10.638784
MA0068.10.0795413
MA0069.10.354782
MA0070.10.345954
MA0071.10.100424
MA0072.10.342425
MA0073.11.33044
MA0074.10.117607
MA0076.10.042375
MA0077.11.60354
MA0078.10.175262
MA0081.10.963299
MA0083.11.72988
MA0084.10.811454
MA0087.10.340509
MA0088.10.0432759
MA0089.10
MA0090.11.09175
MA0091.16.15926
MA0092.10.460323
MA0093.14.13039
MA0095.10
MA0098.10
MA0100.10.127731
MA0101.10.457879
MA0103.10.217657
MA0105.10.00170028
MA0106.10.14308
MA0107.10.479692
MA0108.21.26212
MA0109.10
MA0111.10.051702
MA0113.15.2671
MA0114.10.00922087
MA0115.10.570409
MA0116.11.82858
MA0117.10.396851
MA0119.10.132155
MA0122.10.418111
MA0124.10.533912
MA0125.10.461632
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.10.390959
MA0136.11.85499
MA0139.10.0143415
MA0140.11.63643
MA0141.10.0366436
MA0142.10.222682
MA0143.10.152737
MA0144.10.238059
MA0145.10.2783
MA0146.10.221462
MA0147.12.30896
MA0148.12.64643
MA0149.10.647744
MA0062.20.124078
MA0035.20.0987789
MA0039.20.0561499
MA0138.23.01639
MA0002.20.0224846
MA0137.22.06152
MA0104.21.74063
MA0047.21.95578
MA0112.22.20315
MA0065.20.42037
MA0150.10.0451191
MA0151.10
MA0152.10.335052
MA0153.10.447419
MA0154.10.17951
MA0155.10.0419568
MA0156.10.81154
MA0157.13.27106
MA0158.10
MA0159.11.08772
MA0160.10.0890912
MA0161.10
MA0162.10.001813
MA0163.10.0158653
MA0164.10.160035
MA0080.22.40963
MA0018.21.40052
MA0099.20.102528
MA0079.26.00915e-10
MA0102.20.846442
MA0258.10.387384
MA0259.10.531383
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
POLR2A#5430311.902029956380012.44381677002831e-071.27934726639091e-05



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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