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{{Coexpression_clusters
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|full_id=C2615_Alveolar_Renal_Urothelial_Tracheal_Keratinocyte_renal_Trabecular
|id=C2615
|ontology_enrichment_celltype=CL:0000066!1.28e-56!254;CL:0000548!9.96e-27!679;CL:0000004!9.96e-27!679;CL:0000255!9.96e-27!679;CL:0000012!1.51e-25!682;CL:0000063!1.71e-20!578;CL:0000220!6.48e-17!246;CL:0002321!1.47e-16!248;CL:0000003!4.56e-16!722;CL:0000223!1.66e-15!59;CL:0000076!6.63e-12!62;CL:0002076!3.95e-10!43;CL:1000497!2.15e-08!18;CL:0002518!2.15e-08!18;CL:0000144!2.99e-08!625;CL:1000449!3.29e-07!16;CL:1000507!6.09e-07!12;CL:1000494!6.09e-07!12
|ontology_enrichment_disease=DOID:305!1.46e-25!106;DOID:0050687!6.90e-24!143;DOID:162!3.31e-23!235;DOID:14566!8.64e-22!239;DOID:7!7.41e-10!39
|ontology_enrichment_uberon=UBERON:0004119!1.40e-18!169;UBERON:0000925!1.40e-18!169;UBERON:0006595!1.40e-18!169;UBERON:0005911!1.51e-15!82;UBERON:0000077!1.19e-14!130;UBERON:0001007!2.59e-14!155;UBERON:0001555!2.59e-14!155;UBERON:0007026!2.59e-14!155;UBERON:0000466!5.52e-14!126;UBERON:0003104!7.58e-14!238;UBERON:0009142!7.58e-14!238;UBERON:0002100!5.88e-13!216;UBERON:0009569!6.93e-13!113;UBERON:0001041!3.39e-12!98;UBERON:0004921!5.65e-12!129;UBERON:0004185!5.65e-12!129;UBERON:0001048!1.44e-11!168;UBERON:0005177!5.05e-11!107;UBERON:0003929!1.49e-10!54;UBERON:0005172!2.33e-09!55;UBERON:0005173!2.33e-09!55;UBERON:0006554!2.96e-09!44;UBERON:0002417!3.50e-09!61;UBERON:0000916!3.50e-09!61;UBERON:0000490!8.71e-09!138;UBERON:0001008!1.36e-08!45;UBERON:0000464!1.71e-08!104;UBERON:0003914!1.92e-08!118;UBERON:0002365!4.38e-08!31;UBERON:0002330!4.38e-08!31;UBERON:0009497!4.62e-08!25;UBERON:0000015!4.62e-08!25;UBERON:0002423!4.62e-08!25;UBERON:0006235!4.62e-08!25;UBERON:0004161!4.62e-08!25;UBERON:0007499!5.58e-08!25;UBERON:0008835!7.22e-08!22;UBERON:0003894!7.22e-08!22;UBERON:0005153!1.30e-07!37;UBERON:0002530!2.39e-07!59;UBERON:0004211!3.29e-07!16;UBERON:0001285!3.29e-07!16;UBERON:0007684!3.29e-07!16;UBERON:0003220!3.29e-07!16;UBERON:0004208!3.29e-07!16;UBERON:0009856!3.75e-07!26;UBERON:0005256!3.80e-07!143;UBERON:0001004!3.83e-07!72;UBERON:0000481!4.10e-07!347;UBERON:0000475!4.65e-07!365;UBERON:0009854!5.51e-07!23;UBERON:0009773!6.09e-07!12;UBERON:0001231!6.09e-07!12;UBERON:0004810!6.09e-07!12
}}

Latest revision as of 12:09, 17 September 2013


Full id: C2615_Alveolar_Renal_Urothelial_Tracheal_Keratinocyte_renal_Trabecular



Phase1 CAGE Peaks

Hg19::chr20:361369..361383,+p7@TRIB3
Hg19::chr20:361391..361410,+p2@TRIB3
Hg19::chr20:361478..361491,+p5@TRIB3
Hg19::chr20:361506..361517,+p4@TRIB3


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 cell1.64e-53253
animal cell1.22e-26679
eukaryotic cell1.22e-26679
native cell8.25e-17722
endodermal cell3.34e-1658
embryonic cell1.06e-14250
endo-epithelial cell6.33e-1142
squamous epithelial cell1.34e-1063
kidney cell5.35e-0817
kidney epithelial cell5.35e-0817
kidney tubule cell4.96e-0710
nephron tubule epithelial cell4.96e-0710
epithelial cell of nephron8.21e-0715
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.96e-16160
endoderm3.96e-16160
presumptive endoderm3.96e-16160
endo-epithelium2.77e-1482
organism subdivision2.54e-13264
trunk region element4.28e-13101
digestive system4.91e-12145
digestive tract4.91e-12145
primitive gut4.91e-12145
trunk1.30e-11199
subdivision of trunk2.51e-11112
urinary system structure2.53e-1047
immaterial anatomical entity8.72e-10117
renal system1.16e-0948
subdivision of digestive tract1.24e-09118
gut epithelium1.43e-0954
foregut1.67e-0987
abdomen element4.32e-0854
abdominal segment element4.32e-0854
abdominal segment of trunk5.66e-0860
abdomen5.66e-0860
primordium1.02e-07160
epithelial bud1.41e-0737
nephron tubule epithelium4.96e-0710
exocrine gland5.25e-0731
exocrine system5.25e-0731
epithelial sac6.97e-0725
gland7.63e-0759
nephron epithelium8.21e-0715
renal tubule8.21e-0715
nephron tubule8.21e-0715
nephron8.21e-0715
uriniferous tubule8.21e-0715
nephrogenic mesenchyme8.21e-0715
epithelial fold9.46e-0747
Disease
Ontology termp-valuen
carcinoma9.98e-25106
cancer2.99e-23235
cell type cancer3.74e-23143
disease of cellular proliferation7.42e-22239
disease of anatomical entity6.19e-1039


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
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
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
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
MA0073.10.00636811
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
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.17.71329
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
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.12.31379
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.11.88496
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
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
ATF3#467211.23158726300440.01119559039922220.0411304441291813
BHLHE40#8553222.43590677348870.002891464496853120.0156418554121435
CCNT2#90546.336201576962630.0006203100587215640.00512657768638296
CEBPB#105147.971147625824820.0002476385788090830.00268261855951061
CTCF#1066445.360256373075030.001211145381643620.0081791666675382
CTCFL#140690419.74647435897446.5732084880439e-060.00019310810725255
E2F1#186944.907389214879320.001724022357361790.0106579360116318
ELF1#199744.258097958807540.003041525565781240.0161016772386773
ETS1#211349.728760922202340.0001115955317418140.00154656657903175
GABPB1#255335.300762877136630.01012678824234270.0378699383143094
HEY1#2346244.040111043105710.00375304636917980.018625946101063
HMGN3#932448.178547723350590.0002234570284440470.00248272644613488
RAD21#5885410.35503389545638.6948481184721e-050.00129522356674527
SMC3#9126415.04493284493281.95092670935632e-050.000438366683731637
TAF1#687243.343046285745290.008005664898701650.0322570847359376
TBP#690843.706770687096390.005296377814784350.0244528713407127
TCF7L2#6934410.77017656313737.42969445082454e-050.00115520300543347
TFAP2A#7020416.5186343730451.34240829060362e-050.000326806012732754
TFAP2C#7022410.80922860986027.32289634782688e-050.00114627693595727
YY1#752844.911170749853860.00171871838055440.0106935082179627
ZBTB7A#5134147.35190930787590.000342223540015990.00346903661998738
ZEB1#6935416.88843201754391.22862303393937e-050.000304427428331184



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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