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Coexpression cluster:C488: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:24, 17 September 2013


Full id: C488_biphenotypic_acute_skeletal_hippocampus_Monocytederived_diaphragm_small



Phase1 CAGE Peaks

Hg19::chr10:124894877..124894895,+p@chr10:124894877..124894895
+
Hg19::chr10:124894958..124894963,-p@chr10:124894958..124894963
-
Hg19::chr10:124907645..124907660,+p1@HMX2
Hg19::chr10:124907828..124907837,+p6@HMX2
Hg19::chr10:124907876..124907888,+p5@HMX2
Hg19::chr10:71332711..71332719,+p@chr10:71332711..71332719
+
Hg19::chr10:7453445..7453459,-p1@SFMBT2
Hg19::chr10:7453559..7453566,+p1@AK123101
Hg19::chr15:43531113..43531125,-p@chr15:43531113..43531125
-
Hg19::chr15:43531148..43531194,-p@chr15:43531148..43531194
-
Hg19::chr17:56368264..56368268,+p@chr17:56368264..56368268
+
Hg19::chr17:79792942..79792953,-p2@PPP1R27
Hg19::chr17:79793013..79793019,-p3@PPP1R27
Hg19::chr1:246269774..246269792,-p@chr1:246269774..246269792
-
Hg19::chr1:246271474..246271493,-p@chr1:246271474..246271493
-
Hg19::chr1:246271512..246271521,-p@chr1:246271512..246271521
-
Hg19::chr1:246271543..246271558,-p@chr1:246271543..246271558
-
Hg19::chr5:134788086..134788121,-p3@TIFAB
Hg19::chr8:48626488..48626489,+p@chr8:48626488..48626489
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell7.97e-10108
common myeloid progenitor7.97e-10108
Uber Anatomy
Ontology termp-valuen
medulla oblongata1.51e-083
myelencephalon1.51e-083
future myelencephalon1.51e-083
Disease
Ontology termp-valuen
myeloid leukemia1.07e-3431
leukemia1.34e-2739
syndrome5.13e-231
hematologic cancer4.11e-2151
immune system cancer4.11e-2151
hematopoietic system disease3.24e-122
organ system cancer1.03e-07137
cardiovascular system disease9.63e-074


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)
MA0003.10.11206
MA0004.10.193314
MA0006.10.0925234
MA0007.10.180248
MA0009.10.580032
MA0014.12.23958
MA0017.11.77541
MA0019.10.824541
MA0024.11.21812
MA0025.11.67822
MA0027.12.15732
MA0028.10.332468
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.269828
MA0040.10.507819
MA0041.10.206566
MA0042.10.541224
MA0043.10.580321
MA0046.10.570066
MA0048.10.131175
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.0183725
MA0056.10
MA0057.10.441948
MA0058.10.12994
MA0059.10.129144
MA0060.10.63069
MA0061.10.121714
MA0063.10
MA0066.10.743889
MA0067.10.879057
MA0068.10.213016
MA0069.10.566544
MA0070.10.556335
MA0071.10.674412
MA0072.10.552241
MA0073.10.000856849
MA0074.11.34938
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.129245
MA0083.11.43365
MA0084.11.06048
MA0087.10.550016
MA0088.10.0542435
MA0089.10
MA0090.10.891785
MA0091.10.195166
MA0092.10.504823
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.317957
MA0103.10.295078
MA0105.10.035705
MA0106.10.302526
MA0107.10.214555
MA0108.21.93605
MA0109.10
MA0111.11.48573
MA0113.10.315797
MA0114.10.456488
MA0115.10.805883
MA0116.10.219141
MA0117.10.614633
MA0119.10.762609
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.11.69199
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.792683
MA0140.13.56054
MA0141.11.88893
MA0142.10.407878
MA0143.10.847678
MA0144.10.0508083
MA0145.10.454107
MA0146.10.306103
MA0147.10.0623218
MA0148.10.211171
MA0149.10.230803
MA0062.20.279264
MA0035.20.237534
MA0039.20.810599
MA0138.20.347473
MA0002.20.0346057
MA0137.20.342218
MA0104.20.0384802
MA0047.20.292798
MA0112.20.632219
MA0065.20.156004
MA0150.10.145358
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.11.53519
MA0155.10.236629
MA0156.10.345664
MA0157.10.384449
MA0158.10
MA0159.10.224647
MA0160.10.632864
MA0161.10
MA0162.10.101051
MA0163.10.10617
MA0164.10.32594
MA0080.20.31321
MA0018.20.819991
MA0099.20.681929
MA0079.21.58722
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

No analysis results for this cluster

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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