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Coexpression cluster:C487: 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: C487_CD4_Peripheral_CD8_Natural_CD14_immature_Basophils



Phase1 CAGE Peaks

Hg19::chr10:116285481..116285484,-p@chr10:116285481..116285484
-
Hg19::chr10:116301431..116301440,+p@chr10:116301431..116301440
+
Hg19::chr10:22053811..22053858,-p@chr10:22053811..22053858
-
Hg19::chr12:52980179..52980184,+p@chr12:52980179..52980184
+
Hg19::chr12:53039248..53039257,-p@chr12:53039248..53039257
-
Hg19::chr12:53039641..53039647,+p@chr12:53039641..53039647
+
Hg19::chr12:53039683..53039695,+p@chr12:53039683..53039695
+
Hg19::chr13:100024364..100024401,-p@chr13:100024364..100024401
-
Hg19::chr16:22546145..22546152,+p@chr16:22546145..22546152
+
Hg19::chr17:2166589..2166595,-p@chr17:2166589..2166595
-
Hg19::chr17:44342424..44342435,+p@chr17:44342424..44342435
+
Hg19::chr17:80085902..80085908,+p@chr17:80085902..80085908
+
Hg19::chr20:1267390..1267394,-p@chr20:1267390..1267394
-
Hg19::chr2:238616388..238616397,+p@chr2:238616388..238616397
+
Hg19::chr3:59996534..59996538,-p@chr3:59996534..59996538
-
Hg19::chr3:71527852..71527877,-p@chr3:71527852..71527877
-
Hg19::chr5:141484393..141484402,+p@chr5:141484393..141484402
+
Hg19::chr6:90981633..90981642,-p@chr6:90981633..90981642
-
Hg19::chr7:3501786..3501792,+p@chr7:3501786..3501792
+


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><br><br>

Cell Type
Ontology termp-valuen
CD4-positive, alpha-beta T cell1.14e-336
mature alpha-beta T cell1.52e-2418
alpha-beta T cell1.52e-2418
immature T cell1.52e-2418
mature T cell1.52e-2418
immature alpha-beta T cell1.52e-2418
naive T cell5.50e-183
T cell1.31e-1725
pro-T cell1.31e-1725
single nucleate cell1.94e-173
mononuclear cell1.94e-173
natural killer cell3.48e-173
pro-NK cell3.48e-173
lymphoid lineage restricted progenitor cell1.99e-1452
lymphocyte3.85e-1453
common lymphoid progenitor3.85e-1453
CD4-positive, alpha-beta thymocyte4.53e-141
naive thymus-derived CD4-positive, alpha-beta T cell4.53e-141
mature CD4 single-positive thymocyte4.53e-141
resting double-positive thymocyte4.53e-141
double-positive blast4.53e-141
CD69-positive double-positive thymocyte4.53e-141
CD69-positive, CD4-positive single-positive thymocyte4.53e-141
CD4-positive, CD8-intermediate double-positive thymocyte4.53e-141
CD24-positive, CD4 single-positive thymocyte4.53e-141
nucleate cell1.34e-1355
nongranular leukocyte1.86e-09115
circulating cell3.42e-096
leukocyte8.16e-08136
regulatory T cell9.87e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell9.87e-082
naive regulatory T cell9.87e-082
thymocyte1.12e-072
double negative thymocyte1.12e-072
double-positive, alpha-beta thymocyte1.12e-072
DN4 thymocyte1.12e-072
DN1 thymic pro-T cell1.12e-072
DN2 thymocyte1.12e-072
DN3 thymocyte1.12e-072
immature single positive thymocyte1.12e-072
early T lineage precursor1.12e-072


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)
MA0003.13.71336e-06
MA0004.10.193314
MA0006.10.308609
MA0007.10.180248
MA0009.10.580032
MA0014.10.000501857
MA0017.10.114723
MA0019.10.305657
MA0024.10.485346
MA0025.11.67822
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.743126
MA0040.10.507819
MA0041.10.595574
MA0042.10.541224
MA0043.10.580321
MA0046.10.570066
MA0048.10.00932809
MA0050.10.184533
MA0051.10.266537
MA0052.11.27353
MA0055.10.106762
MA0056.10
MA0057.10.0434899
MA0058.10.12994
MA0059.10.129144
MA0060.10.0387582
MA0061.10.121714
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.213016
MA0069.10.566544
MA0070.10.556335
MA0071.10.674412
MA0072.10.552241
MA0073.10.000103775
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.915792
MA0081.10.80621
MA0083.11.43365
MA0084.11.06048
MA0087.10.550016
MA0088.10.0542435
MA0089.10
MA0090.10.455738
MA0091.10.195166
MA0092.10.168981
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.10.295078
MA0105.10.035705
MA0106.10.302526
MA0107.10.214555
MA0108.21.10489
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.0569149
MA0115.10.805883
MA0116.10.219141
MA0117.11.49188
MA0119.10.379868
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.0257123
MA0140.10.238066
MA0141.10.801079
MA0142.10.407878
MA0143.10.315941
MA0144.10.0508083
MA0145.10.0209869
MA0146.10.00163852
MA0147.10.0623218
MA0148.10.211171
MA0149.10.230803
MA0062.20.027823
MA0035.20.237534
MA0039.20.00730638
MA0138.20.347473
MA0002.22.30281
MA0137.20.105044
MA0104.20.0384802
MA0047.20.292798
MA0112.20.0184087
MA0065.20.003771
MA0150.10.446185
MA0151.10
MA0152.10.243034
MA0153.10.67139
MA0154.10.00634321
MA0155.10.00260895
MA0156.10.345664
MA0157.10.384449
MA0158.10
MA0159.10.224647
MA0160.11.18515
MA0161.10
MA0162.10.00153143
MA0163.10.000591497
MA0164.10.32594
MA0080.20.646623
MA0018.20.30364
MA0099.20.243305
MA0079.25.53374e-08
MA0102.21.09681
MA0258.10.046907
MA0259.10.0662172
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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