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Coexpression cluster:C721: Difference between revisions

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{{Coexpression_clusters
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|full_id=C721_CD4_CD14_Neutrophils_Natural_CD8_CD19_Monocytederived
|id=C721
}}

Latest revision as of 11:29, 17 September 2013


Full id: C721_CD4_CD14_Neutrophils_Natural_CD8_CD19_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:3819310..3819325,-p5@KLF6
Hg19::chr10:3820389..3820459,-p@chr10:3820389..3820459
-
Hg19::chr10:3821267..3821288,-p@chr10:3821267..3821288
-
Hg19::chr10:3821390..3821446,-p@chr10:3821390..3821446
-
Hg19::chr10:3821469..3821544,-p@chr10:3821469..3821544
-
Hg19::chr10:3823938..3823954,-p13@KLF6
Hg19::chr10:3824206..3824226,-p10@KLF6
Hg19::chr10:3824229..3824253,-p7@KLF6
Hg19::chr10:3824309..3824321,-p15@KLF6
Hg19::chr19:49377180..49377237,-p@chr19:49377180..49377237
-
Hg19::chr4:103471349..103471366,+p@chr4:103471349..103471366
+


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

No GOStat results

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
bone marrow4.61e-1776
hematopoietic system5.44e-1798
blood island5.44e-1798
hemolymphoid system1.03e-15108
bone element6.20e-1582
skeletal element6.98e-1490
immune system3.16e-1393
skeletal system8.01e-13100
lateral plate mesoderm6.12e-09203
mesoderm1.06e-08315
mesoderm-derived structure1.06e-08315
presumptive mesoderm1.06e-08315
musculoskeletal system5.06e-08167


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)
MA0003.10.00460185
MA0004.10.92264
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.00227771
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.12.43819
MA0051.11.96019
MA0052.10.716602
MA0055.10.136684
MA0056.10
MA0057.10.0465155
MA0058.12.07342
MA0059.11.34253
MA0060.10.38025
MA0061.10.100525
MA0063.10
MA0066.11.12972
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.000309691
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.11.15029
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.11.2452
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.637178
MA0140.10.405425
MA0141.10.726533
MA0142.11.46715
MA0143.10.498176
MA0144.12.00452
MA0145.11.19384
MA0146.10.184736
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.20.00623756
MA0138.20.534556
MA0002.20.725804
MA0137.20.649788
MA0104.20.378829
MA0047.20.47109
MA0112.20.106997
MA0065.20.11899
MA0150.10.286461
MA0151.10
MA0152.11.86388
MA0153.10.887528
MA0154.10.153348
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.00253231
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.28.76424e-07
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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#5430101.952230160507340.00304073181841430.0161326385767524



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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