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

Latest revision as of 11:33, 17 September 2013


Full id: C920_anaplastic_adult_hereditary_cord_hairy_immature_xeroderma



Phase1 CAGE Peaks

Hg19::chr17:53535935..53535939,+p@chr17:53535935..53535939
+
Hg19::chr17:80317121..80317128,+p1@TEX19
Hg19::chr1:12123219..12123228,+p6@TNFRSF8
Hg19::chr1:12123317..12123328,+p8@TNFRSF8
Hg19::chr1:12123343..12123367,+p1@TNFRSF8
Hg19::chr1:12123379..12123405,+p2@TNFRSF8
Hg19::chr1:12123414..12123445,+p3@TNFRSF8
Hg19::chr1:12124073..12124086,+p@chr1:12124073..12124086
+
Hg19::chr5:129083784..129083814,+p1@KIAA1024L


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:0045554regulation of TRAIL biosynthetic process0.000551925114800424
GO:0032639TRAIL production0.000551925114800424
GO:0045556positive regulation of TRAIL biosynthetic process0.000551925114800424
GO:0045553TRAIL biosynthetic process0.000551925114800424
GO:0042535positive regulation of tumor necrosis factor biosynthetic process0.00220770045920169
GO:0042533tumor necrosis factor biosynthetic process0.00252308623908765
GO:0042534regulation of tumor necrosis factor biosynthetic process0.00252308623908765
GO:0032640tumor necrosis factor production0.00358751324620275
GO:0042108positive regulation of cytokine biosynthetic process0.0100573020919188
GO:0045727positive regulation of translation0.0103026021429412
GO:0042035regulation of cytokine biosynthetic process0.0103026021429412
GO:0031328positive regulation of cellular biosynthetic process0.0103026021429412
GO:0042089cytokine biosynthetic process0.0103026021429412
GO:0042107cytokine metabolic process0.0103026021429412
GO:0009891positive regulation of biosynthetic process0.0103026021429412
GO:0051247positive regulation of protein metabolic process0.011728408689509
GO:0001816cytokine production0.0146747148170466
GO:0006417regulation of translation0.0225676046940618
GO:0031326regulation of cellular biosynthetic process0.0231227574411125
GO:0009889regulation of biosynthetic process0.0236539334914467
GO:0008285negative regulation of cell proliferation0.0236539334914467
GO:0043065positive regulation of apoptosis0.0247646399336538
GO:0043068positive regulation of programmed cell death0.0247646399336538
GO:0031325positive regulation of cellular metabolic process0.0335754444836924
GO:0009893positive regulation of metabolic process0.0345284351819145
GO:0051246regulation of protein metabolic process0.035832676683966
GO:0042127regulation of cell proliferation0.0383485746431702
GO:0042981regulation of apoptosis0.0438494987758682
GO:0043067regulation of programmed cell death0.0438494987758682



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
testis1.12e-078
Disease
Ontology termp-valuen
hematologic cancer4.46e-2351
immune system cancer4.46e-2351
lymphoma2.18e-1310
leukemia2.42e-1239
chronic leukemia1.02e-108
myeloid leukemia1.65e-0731


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)
MA0003.10.0913842
MA0004.11.87712
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.0956087
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.95759
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.0725989
MA0058.11.56347
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.13.03625
MA0069.10.856287
MA0070.11.96957
MA0071.10.47692
MA0072.10.840664
MA0073.11.21679
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.11.66392
MA0091.10.417885
MA0092.10.381858
MA0093.11.35827
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.11.77226
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.13.13035
MA0145.10.046841
MA0146.10.175555
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.323611
MA0138.20.608783
MA0002.20.46405
MA0137.22.18049
MA0104.20.161609
MA0047.20.542971
MA0112.20.166662
MA0065.20.0483532
MA0150.11.64445
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.12.33732
MA0155.10.156896
MA0156.10.785298
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0533066
MA0163.12.38182
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.22.0981
MA0079.20.741908
MA0102.21.41188
MA0258.10.180288
MA0259.11.82941
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
E2F6#187673.902232235764630.0003067423599492730.00316278658611336
EBF1#187965.937644564379340.0001242436507924170.00165614328591056
ELF1#199762.838731972538360.007207863124148630.0298592684472238
JUND#372753.885924412150570.004544089270401160.0214810183909576
MAFK#7975618.06715542521991.92160575057211e-071.04744563144051e-05
MAX#414964.301703672671410.0007597563851723660.00596917152719602
SIN3A#2594253.004935959341740.01401618817346520.0491979793186979
USF1#739153.534166265115530.00692296754081810.0293103537779918



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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