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Coexpression cluster:C497: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.166404198976881,0

Latest revision as of 11:24, 17 September 2013


Full id: C497_skeletal_Neutrophils_renal_Cardiac_heart_Hepatocyte_Olfactory



Phase1 CAGE Peaks

Hg19::chr11:65199679..65199734,+p@chr11:65199679..65199734
+
Hg19::chr11:65199741..65199835,+p@chr11:65199741..65199835
+
Hg19::chr11:65199879..65200105,+p@chr11:65199879..65200105
+
Hg19::chr11:65200183..65200211,+p@chr11:65200183..65200211
+
Hg19::chr11:65200284..65200319,+p@chr11:65200284..65200319
+
Hg19::chr11:65200820..65200841,+p@chr11:65200820..65200841
+
Hg19::chr11:65200844..65200884,+p@chr11:65200844..65200884
+
Hg19::chr11:65200886..65200948,+p@chr11:65200886..65200948
+
Hg19::chr11:65200963..65201054,+p@chr11:65200963..65201054
+
Hg19::chr11:65201385..65201406,+p@chr11:65201385..65201406
+
Hg19::chr11:65203627..65203734,+p@chr11:65203627..65203734
+
Hg19::chr11:65204834..65204909,+p@chr11:65204834..65204909
+
Hg19::chr11:65205206..65205240,+p@chr11:65205206..65205240
+
Hg19::chr11:65205691..65205817,+p@chr11:65205691..65205817
+
Hg19::chr11:65206622..65206685,+p2@AK129631
Hg19::chr11:65207246..65207264,+p1@AK129631
Hg19::chr11:65207660..65207678,+p@chr11:65207660..65207678
+
Hg19::chr11:65208946..65209001,+p@chr11:65208946..65209001
+
Hg19::chr11:65209035..65209049,+p@chr11:65209035..65209049
+


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
adult organism1.62e-13114
hematopoietic system5.98e-0998
blood island5.98e-0998
hemolymphoid system2.47e-08108
bone marrow1.78e-0776
organ1.82e-07503


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)
MA0003.12.41061e-07
MA0004.10.563888
MA0006.10.0925234
MA0007.10.180248
MA0009.10.580032
MA0014.14.97928e-05
MA0017.10.114723
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.269828
MA0040.10.507819
MA0041.12.48925
MA0042.11.63578
MA0043.10.580321
MA0046.10.570066
MA0048.10.0472517
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.00470761
MA0056.10
MA0057.10.00844127
MA0058.10.12994
MA0059.10.129144
MA0060.10.0387582
MA0061.10.029485
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.409781
MA0069.11.3907
MA0070.10.556335
MA0071.12.72227
MA0072.10.552241
MA0073.16.83377e-06
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.405301
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.0542435
MA0089.10
MA0090.10.891785
MA0091.11.07936
MA0092.10.168981
MA0093.10.313082
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.10.614572
MA0105.10.035705
MA0106.10.302526
MA0107.10.0591705
MA0108.20.432749
MA0109.10
MA0111.10.477838
MA0113.10.315797
MA0114.10.0569149
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.13.66975
MA0136.10.27535
MA0139.10.0257123
MA0140.10.238066
MA0141.10.801079
MA0142.11.05085
MA0143.10.315941
MA0144.10.0508083
MA0145.10.0209869
MA0146.12.87274e-05
MA0147.10.0623218
MA0148.10.606512
MA0149.10.230803
MA0062.20.027823
MA0035.20.237534
MA0039.26.91533e-06
MA0138.20.347473
MA0002.20.0346057
MA0137.20.105044
MA0104.20.0384802
MA0047.21.44762
MA0112.20.136364
MA0065.20.003771
MA0150.10.446185
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.00634321
MA0155.10.0530942
MA0156.10.106343
MA0157.10.99963
MA0158.10
MA0159.10.224647
MA0160.10.632864
MA0161.10
MA0162.10.00153143
MA0163.15.97641e-05
MA0164.10.32594
MA0080.20.0942207
MA0018.20.30364
MA0099.20.243305
MA0079.21.13453e-13
MA0102.21.09681
MA0258.10.399676
MA0259.10.235101
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#5430192.147453176558074.9316078952508e-072.31172440292683e-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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