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{{Coexpression_clusters
{
|full_id=C1197_hepatoma_Hepatocyte_liver_argyrophil_hepatocellular_gastrointestinal_mesothelioma
 

Latest revision as of 11:39, 17 September 2013


Full id: C1197_hepatoma_Hepatocyte_liver_argyrophil_hepatocellular_gastrointestinal_mesothelioma



Phase1 CAGE Peaks

Hg19::chr14:23445892..23445897,-p17@AJUBA
Hg19::chr14:23445927..23445936,-p15@AJUBA
Hg19::chr16:52417646..52417654,-p@chr16:52417646..52417654
-
Hg19::chr2:73248062..73248100,-p21@SFXN5
Hg19::chr5:147209673..147209678,-p@chr5:147209673..147209678
-
Hg19::chr6:50061315..50061323,+p1@ENST00000415106
Hg19::chr9:116840728..116840744,-p2@AMBP


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:0030568plasmin inhibitor activity0.00260500985625729
GO:0046904calcium oxalate binding0.00260500985625729
GO:0019862IgA binding0.00260500985625729
GO:0019855calcium channel inhibitor activity0.00260500985625729
GO:0046329negative regulation of JNK cascade0.00260500985625729
GO:0042167heme catabolic process0.00260500985625729
GO:0030304trypsin inhibitor activity0.00260500985625729
GO:0046149pigment catabolic process0.00260500985625729
GO:0006787porphyrin catabolic process0.00347324422754211
GO:0033015tetrapyrrole catabolic process0.00347324422754211
GO:0050777negative regulation of immune response0.00496141229839008
GO:0002683negative regulation of immune system process0.00496141229839008
GO:0008200ion channel inhibitor activity0.00496141229839008
GO:0016248channel inhibitor activity0.00496141229839008
GO:0005246calcium channel regulator activity0.0050936416448709
GO:0019865immunoglobulin binding0.00694536373294039
GO:0046328regulation of JNK cascade0.00767588960040256
GO:0042168heme metabolic process0.00767588960040256
GO:0018298protein-chromophore linkage0.00767588960040256
GO:0051241negative regulation of multicellular organismal process0.00868055438216479
GO:0006778porphyrin metabolic process0.00991990324056249
GO:0033013tetrapyrrole metabolic process0.0108678033134421
GO:0016247channel regulator activity0.0108678033134421
GO:0042440pigment metabolic process0.012149734272869
GO:0051187cofactor catabolic process0.0138837746380827
GO:0019748secondary metabolic process0.0141501450216093
GO:0006826iron ion transport0.0146535844609547
GO:0007254JNK cascade0.01611153515917
GO:0031098stress-activated protein kinase signaling pathway0.0162732133377396
GO:0007565female pregnancy0.018734537648372
GO:0050776regulation of immune response0.0206109159829187
GO:0002682regulation of immune system process0.0206109159829187
GO:0032403protein complex binding0.0206109159829187
GO:0000041transition metal ion transport0.0206109159829187
GO:0009968negative regulation of signal transduction0.0206109159829187
GO:0046483heterocycle metabolic process0.0250383882725595
GO:0000165MAPKKK cascade0.0281013347524844
GO:0042803protein homodimerization activity0.0288177222531866
GO:0004867serine-type endopeptidase inhibitor activity0.0298515414307917
GO:0006810transport0.0406471491569161
GO:0015674di-, tri-valent inorganic cation transport0.0406471491569161
GO:0004866endopeptidase inhibitor activity0.0406471491569161
GO:0051234establishment of localization0.0406471491569161
GO:0030414protease inhibitor activity0.0418333476446704
GO:0051239regulation of multicellular organismal process0.042588301530179
GO:0020037heme binding0.0427626175573073
GO:0046906tetrapyrrole binding0.0427626175573073
GO:0051179localization0.0427626175573073
GO:0022414reproductive process0.043047415010481
GO:0051704multi-organism process0.046040255562797
GO:0051186cofactor metabolic process0.046486109454568
GO:0042802identical protein binding0.0477151929368722
GO:0046983protein dimerization activity0.0477151929368722
GO:0007243protein kinase cascade0.0481040101179392



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
metabolising cell1.39e-4712
endopolyploid cell1.39e-4712
parenchymal cell1.39e-4712
polyploid cell1.39e-4712
hepatocyte1.39e-4712
endodermal cell2.31e-1558
Uber Anatomy
Ontology termp-valuen
hepatic diverticulum1.70e-5222
liver primordium1.70e-5222
digestive tract diverticulum3.62e-5023
liver2.27e-4919
digestive gland2.27e-4919
liver bud2.27e-4919
epithelial sac4.52e-4625
epithelium of foregut-midgut junction4.52e-4625
anatomical boundary4.52e-4625
hepatobiliary system4.52e-4625
foregut-midgut junction4.52e-4625
septum transversum4.52e-4625
sac2.93e-4426
exocrine gland6.47e-3031
exocrine system6.47e-3031
gut epithelium7.62e-3054
endocrine gland2.18e-2635
abdomen element4.97e-2554
abdominal segment element4.97e-2554
abdominal segment of trunk2.16e-2260
abdomen2.16e-2260
endocrine system2.63e-2045
endo-epithelium3.86e-1982
gland8.75e-1959
trunk region element9.99e-13101
subdivision of digestive tract1.08e-12118
foregut2.18e-1287
subdivision of trunk2.48e-11112
mesenchyme9.96e-11160
entire embryonic mesenchyme9.96e-11160
trunk mesenchyme2.73e-10122
digestive system4.84e-10145
digestive tract4.84e-10145
primitive gut4.84e-10145
unilaminar epithelium6.97e-10148
endoderm-derived structure5.98e-09160
endoderm5.98e-09160
presumptive endoderm5.98e-09160
immaterial anatomical entity7.10e-09117
epithelial tube7.10e-09117
trunk2.89e-08199
Disease
Ontology termp-valuen
disease of anatomical entity1.66e-0739


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)
MA0003.10.0462779
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.991615
MA0019.11.57204
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.11.01052
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.11.47685
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.11.39306
MA0072.10.942461
MA0073.10.00958848
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.21.95102
MA0065.20.591589
MA0150.11.92997
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.21.40221
MA0079.20.0015479
MA0102.21.51913
MA0258.11.97124
MA0259.10.289405
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#105144.554941500471320.006321080333068460.0275299127983877
EP300#203376.77394172622321.52695018318475e-065.86082874610924e-05
FOSL2#235537.255800259097870.006020775093849750.0269849682442097
FOXA1#316969.498359785187533.4851329158676e-060.000115881501623781
FOXA2#3170621.11182607371313.02035985915038e-082.04700430454125e-06
HDAC2#306659.582585883304474.24859153994197e-050.00076005250400822
HNF4A#317239.913838726980150.002478654821661540.0139228866196692
HNF4G#3174312.32289536847720.001324450221997230.00879254110953275
MAFK#7975311.61459991621280.001571626617440920.00996533982750971
TCF7L2#693446.154386607507050.002064676148138040.0119709494384827



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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