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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:27, 17 September 2013


Full id: C644_chronic_Reticulocytes_acute_CD34_leukemia_liver_schwannoma



Phase1 CAGE Peaks

Hg19::chr10:119184702..119184711,+p1@ENST00000549104
Hg19::chr11:119994013..119994021,-p50@TRIM29
Hg19::chr11:13804110..13804121,-p@chr11:13804110..13804121
-
Hg19::chr11:33903432..33903464,-p@chr11:33903432..33903464
-
Hg19::chr11:33903469..33903500,-p@chr11:33903469..33903500
-
Hg19::chr11:5264817..5264828,-p4@HBBP1
Hg19::chr11:5264837..5264870,-p1@HBBP1
Hg19::chr11:5264874..5264909,-p2@HBBP1
Hg19::chr11:5264923..5264932,-p6@HBBP1
Hg19::chr13:52569530..52569556,-p@chr13:52569530..52569556
-
Hg19::chr19:12997072..12997102,-p@chr19:12997072..12997102
-
Hg19::chr19:13189413..13189435,+p@chr19:13189413..13189435
+
Hg19::chr8:41655080..41655089,-p10@ANK1


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:0045199maintenance of epithelial cell polarity0.00214879681956168
GO:0030507spectrin binding0.00214879681956168
GO:0030011maintenance of cell polarity0.00214879681956168
GO:0035090maintenance of apical/basal cell polarity0.00214879681956168
GO:0045197establishment and/or maintenance of epithelial cell polarity0.00552490824291214
GO:0008093cytoskeletal adaptor activity0.00552490824291214
GO:0035088establishment and/or maintenance of apical/basal cell polarity0.00552490824291214
GO:0016528sarcoplasm0.0119337188304714
GO:0016529sarcoplasmic reticulum0.0119337188304714
GO:0007163establishment and/or maintenance of cell polarity0.0124580687034563
GO:0060090molecular adaptor activity0.0234214083346067
GO:0005200structural constituent of cytoskeleton0.0280653228297728
GO:0016323basolateral plasma membrane0.0280653228297728
GO:0006887exocytosis0.0340191124462199



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>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.49e-087
immune organ2.49e-087
Disease
Ontology termp-valuen
chronic leukemia7.23e-598
myeloid leukemia2.68e-5031
leukemia8.99e-4039
hematologic cancer3.66e-3051
immune system cancer3.66e-3051
chronic myeloid leukemia4.73e-151
organ system cancer2.27e-10137


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)
MA0003.10.186635
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.0622624
MA0017.11.09607
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.11.00626
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.131159
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.531463
MA0056.10
MA0057.10.294933
MA0058.10.219229
MA0059.10.218203
MA0060.10.2996
MA0061.10.255087
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.196125
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.10.0072687
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.623454
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.337854
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.517741
MA0103.10.489275
MA0105.10.0255214
MA0106.10.424592
MA0107.11.26082
MA0108.20.568002
MA0109.10
MA0111.10.708492
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.10.782807
MA0117.10.76111
MA0119.10.593096
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.13.69665
MA0139.10.0663461
MA0140.12.49888
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.714233
MA0145.10.194261
MA0146.10.312689
MA0147.10.126316
MA0148.10.319209
MA0149.10.342334
MA0062.20.527542
MA0035.21.65207
MA0039.20.332438
MA0138.20.474787
MA0002.20.0821804
MA0137.20.54754
MA0104.20.088751
MA0047.20.413608
MA0112.20.180347
MA0065.23.2483
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.11.54414
MA0155.10.845872
MA0156.11.05198
MA0157.10.515488
MA0158.10
MA0159.10.126752
MA0160.10.884483
MA0161.10
MA0162.10.00205586
MA0163.10.572543
MA0164.10.450848
MA0080.22.97764
MA0018.20.425847
MA0099.20.356906
MA0079.20.05427
MA0102.21.25596
MA0258.10.335505
MA0259.10.132107
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
GATA1#262366.258603758677130.0001749511264227230.00212808300634321
SMARCA4#6597224.11783127813660.003026596196368890.0160690702126262
TAL1#688649.190343593058530.0007038605141735960.00565857041334587



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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