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{{Coexpression_clusters
{
|full_id=C2125_gastric_signet_Lens_Ciliary_lung_Hepatocyte_kidney

Latest revision as of 11:59, 17 September 2013


Full id: C2125_gastric_signet_Lens_Ciliary_lung_Hepatocyte_kidney



Phase1 CAGE Peaks

Hg19::chr11:27494245..27494278,-p5@LGR4
Hg19::chr11:27494279..27494308,-p3@LGR4
Hg19::chr11:27494309..27494328,-p2@LGR4
Hg19::chr11:27494329..27494347,-p1@LGR4


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
epithelial cell7.62e-07253
Uber Anatomy
Ontology termp-valuen
organ1.06e-16503
multi-cellular organism2.14e-15656
multi-tissue structure7.70e-15342
anatomical cluster1.55e-14373
primordium4.59e-12160
anatomical system9.48e-12624
anatomical group1.47e-11625
embryo1.96e-09592
organ system subdivision1.26e-08223
adult organism8.37e-08114
compound organ1.21e-0768
developing anatomical structure1.21e-07581
organ part2.35e-07218
reproductive organ2.55e-0748
epithelium2.73e-07306
cell layer3.30e-07309
digestive system3.59e-07145
digestive tract3.59e-07145
primitive gut3.59e-07145
ectoderm-derived structure3.80e-07171
ectoderm3.80e-07171
presumptive ectoderm3.80e-07171
external genitalia4.98e-0722
endoderm-derived structure5.23e-07160
endoderm5.23e-07160
presumptive endoderm5.23e-07160
gonad5.69e-0721
indifferent external genitalia5.69e-0721
indifferent gonad5.69e-0721
gonad primordium5.69e-0721
structure with developmental contribution from neural crest9.39e-07132
Disease
Ontology termp-valuen
cell type cancer4.82e-10143
carcinoma1.09e-08106


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.12.02743
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.15.89804
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.186.2906
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.15.34177
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CEBPB#105147.971147625824820.0002476385788090830.00267595711663133
HEY1#2346244.040111043105710.00375304636917980.0185518936837736
IRF3#3661446.98195221148962.04940266214005e-071.10101627896731e-05
MXI1#460149.96157162875930.0001015224754950450.00142111055062686
NFYB#4801416.75979325353651.26678572070404e-050.000311005721402467
PBX3#5090421.91451268674414.33289161192893e-060.000135974419188175
POU2F2#545249.106124057742520.000145395665174930.00188025976661769
RFX5#5993412.04791082719514.74457429336527e-050.00082531411496465
SIN3A#2594245.408884726815140.001168172384885160.00794133669888829
SMARCB1#6598418.25271578115749.00423392720929e-060.00024075606429181
TAF1#687243.343046285745290.008005664898701650.0321220037786892
TAF7#6879411.43306940492395.85061525419808e-050.000967282581182829
TBP#690843.706770687096390.005296377814784350.0243473921650716



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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