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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:24, 17 September 2013


Full id: C507_splenic_hairy_b_cord_B_xeroderma_mycosis



Phase1 CAGE Peaks

Hg19::chr10:79464313..79464317,-p@chr10:79464313..79464317
-
Hg19::chr10:79468189..79468192,-p@chr10:79468189..79468192
-
Hg19::chr10:79471157..79471172,-p@chr10:79471157..79471172
-
Hg19::chr10:85931581..85931600,-p3@ENST00000514797
p3@uc001kct.2
Hg19::chr12:114400163..114400173,-p@chr12:114400163..114400173
-
Hg19::chr14:75981948..75981957,+p@chr14:75981948..75981957
+
Hg19::chr14:75982124..75982133,+p@chr14:75982124..75982133
+
Hg19::chr14:75982154..75982176,+p@chr14:75982154..75982176
+
Hg19::chr14:75982181..75982197,+p@chr14:75982181..75982197
+
Hg19::chr17:33396527..33396551,-p7@RFFL
Hg19::chr17:33396568..33396595,-p8@RFFL
Hg19::chr17:33396602..33396623,-p5@RFFL
Hg19::chr1:25799275..25799284,+p@chr1:25799275..25799284
+
Hg19::chr2:111562758..111562766,+p5@ACOXL
Hg19::chr2:231454349..231454360,-p@chr2:231454349..231454360
-
Hg19::chr2:242067121..242067130,-p16@PASK
Hg19::chr8:10389502..10389527,-p@chr8:10389502..10389527
-
Hg19::chr8:22576899..22576911,+p@chr8:22576899..22576911
+


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>

Uber Anatomy
Ontology termp-valuen
tonsil2.07e-131
mucosa-associated lymphoid tissue2.07e-131
lymphoid tissue2.07e-131
tonsillar ring2.07e-131
umbilical cord7.54e-1210
blastocyst7.54e-1210
blastula7.54e-1210
bilaminar disc7.54e-1210
inner cell mass7.54e-1210
cleaving embryo7.54e-1210
connecting stalk7.54e-1210
inner cell mass derived epiblast7.54e-1210
extraembryonic mesoderm7.54e-1210
blood4.43e-0815
haemolymphatic fluid4.43e-0815
organism substance4.43e-0815
Disease
Ontology termp-valuen
lymphoma8.83e-3110
genetic disease9.73e-141
monogenic disease9.73e-141
xeroderma pigmentosum9.73e-141
anemia1.25e-131
non-Hodgkin lymphoma1.42e-131
cutaneous T cell lymphoma1.42e-131
mycosis fungoides1.42e-131
hematologic cancer1.86e-0851
immune system cancer1.86e-0851
hematopoietic system disease1.87e-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)
MA0003.10.00772785
MA0004.10.207008
MA0006.10.334079
MA0007.10.193512
MA0009.10.600198
MA0014.10.122675
MA0017.10.395274
MA0019.10.322194
MA0024.10.50459
MA0025.10.725013
MA0027.12.18072
MA0028.10.111328
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.10.285594
MA0040.10.527306
MA0041.10.220669
MA0042.10.573464
MA0043.10.60049
MA0046.10.590147
MA0048.10.305316
MA0050.10.197941
MA0051.10.282227
MA0052.10.530811
MA0055.10.369682
MA0056.10
MA0057.10.288482
MA0058.10.141262
MA0059.10.433767
MA0060.10.0444001
MA0061.13.45072
MA0063.10
MA0066.10.285934
MA0067.10.900956
MA0068.10.0967272
MA0069.10.586593
MA0070.11.41126
MA0071.10.255111
MA0072.11.40255
MA0073.10.00165096
MA0074.10.281628
MA0076.10.151641
MA0077.10.565087
MA0078.10.363755
MA0081.10.140536
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.10.277816
MA0089.10
MA0090.10.161293
MA0091.10.208918
MA0092.10.181853
MA0093.10.338722
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.11.15589
MA0103.10.320022
MA0105.11.30924
MA0106.10.854542
MA0107.13.02597
MA0108.20.451357
MA0109.10
MA0111.10.170509
MA0113.10.332535
MA0114.10.495259
MA0115.10.827474
MA0116.10.516883
MA0117.10.635078
MA0119.10.407815
MA0122.10.659244
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.10.379172
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.10.291242
MA0139.11.68229
MA0140.10.253051
MA0141.10.430939
MA0142.10.426146
MA0143.10.332682
MA0144.10.459643
MA0145.10.319303
MA0146.10.050005
MA0147.10.0698742
MA0148.10.225411
MA0149.10.245595
MA0062.20.0323736
MA0035.20.252505
MA0039.29.54563e-05
MA0138.20.364793
MA0002.20.999186
MA0137.20.743725
MA0104.20.0440964
MA0047.20.309071
MA0112.20.0713977
MA0065.21.39481
MA0150.12.12407
MA0151.10
MA0152.10.258148
MA0153.10.692238
MA0154.11.28584
MA0155.10.446769
MA0156.10.116546
MA0157.10.402372
MA0158.10
MA0159.10.246493
MA0160.10.236884
MA0161.10
MA0162.10.214564
MA0163.10.218679
MA0164.10.342871
MA0080.20.691565
MA0018.20.320136
MA0099.20.716923
MA0079.22.23912e-07
MA0102.21.11935
MA0258.10.196984
MA0259.10.0740439
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
BATF#10538810.82568968546832.42930653961336e-071.27302732408771e-05
BCL11A#53335711.0325658736251.52168798019066e-065.85353852534559e-05
BCL3#602713.4349844236764.07451111572284e-071.96100399269575e-05
CTCFL#14069055.485131766381770.001635351861265640.0102339572795687
EBF1#1879115.442840850681065.31868622722255e-072.47870714361846e-05
IRF4#366267.304837562248040.0001039351690544030.00145235283929258
MEF2A#420544.165162424365350.01356346165085610.0478792121731143
NFKB1#4790113.353816537007346.54334929204358e-050.00106164495372338
PAX5#5079103.705314183987687.81914617588767e-050.00119880183127354
POU2F2#545294.553062028871264.44118401900389e-050.000787358373384395
RAD21#588574.026957626010790.0009506084120696660.00684504908633094
SP1#666782.53261394584040.007368112951132010.0304602916717443
SPI1#668894.102161754261360.0001019326238867080.00142608724797105
TCF12#693895.317232451093211.2632268459797e-050.000311376324208811



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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