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{{Coexpression_clusters
{
|full_id=C2145_Mesenchymal_Alveolar_Renal_Placental_nonsmall_Bronchial_left
 

Latest revision as of 11:59, 17 September 2013


Full id: C2145_Mesenchymal_Alveolar_Renal_Placental_nonsmall_Bronchial_left



Phase1 CAGE Peaks

Hg19::chr11:62439136..62439162,+p1@C11orf83
Hg19::chr17:73900954..73901003,-p1@MRPL38
Hg19::chr17:79670440..79670524,+p1@MRPL12
p1@SLC25A10
Hg19::chr8:145149957..145150006,+p1@CYC1


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:0005739mitochondrion0.00246685015740525
GO:0045155electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity0.0085656256290494
GO:0006390transcription from mitochondrial promoter0.0142747820013017
GO:0044429mitochondrial part0.0214058702371865
GO:0000315organellar large ribosomal subunit0.0214058702371865
GO:0005762mitochondrial large ribosomal subunit0.0214058702371865
GO:0005840ribosome0.0255028847072952
GO:0044444cytoplasmic part0.0299280631346191
GO:0030529ribonucleoprotein complex0.0354431211698454
GO:0000313organellar ribosome0.0396560987964519
GO:0005761mitochondrial ribosome0.0396560987964519



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 cell5.90e-28253
embryonic cell1.20e-15250
animal cell6.40e-08679
eukaryotic cell6.40e-08679
endodermal cell5.84e-0758
Uber Anatomy
Ontology termp-valuen
trunk3.18e-13199
organism subdivision8.91e-13264
trunk region element7.33e-12101
foregut4.07e-1187
unilaminar epithelium4.23e-11148
mesenchyme1.61e-10160
entire embryonic mesenchyme1.61e-10160
segment of respiratory tract1.63e-1047
multi-tissue structure2.02e-09342
epithelial tube2.51e-09117
respiratory primordium3.20e-0938
endoderm of foregut3.20e-0938
subdivision of digestive tract4.47e-09118
subdivision of trunk5.12e-09112
endoderm-derived structure1.60e-08160
endoderm1.60e-08160
presumptive endoderm1.60e-08160
primordium2.47e-08160
trunk mesenchyme4.33e-08122
respiratory tract7.13e-0854
digestive system8.11e-08145
digestive tract8.11e-08145
primitive gut8.11e-08145
epithelial vesicle1.31e-0778
organ segment1.76e-0798
cell layer1.83e-07309
epithelium2.11e-07306
compound organ2.61e-0768
anatomical cluster3.22e-07373
respiratory system6.13e-0774
Disease
Ontology termp-valuen
cancer2.41e-26235
disease of cellular proliferation3.71e-25239
cell type cancer1.19e-18143
carcinoma1.16e-15106
organ system cancer4.06e-11137
hematologic cancer6.41e-0951
immune system cancer6.41e-0951
myeloid leukemia4.53e-0731
leukemia4.73e-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)
MA0003.13.49532
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
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
MA0073.12.83685
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
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
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.01976
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
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.98779
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
MA0154.10.649108
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.5408
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
BCLAF1#9774210.82632380506090.01202203816432580.0436416282184227
BRCA1#672210.09211532161190.0137713969900260.048460895927805
CCNT2#90546.336201576962630.0006203100587215640.00511282157863006
E2F1#186944.907389214879320.001724022357361790.010626485539454
E2F6#187645.017155731697390.00157802193473060.00995031291682237
EGR1#195844.988179094810140.001615011500076050.0101273002735781
ELK4#2005312.1767612438510.0008912632577620610.00663548926271827
ETS1#211337.296570691651750.00400857377511390.0191971495093141
GABPB1#255347.067683836182170.0004006876864423170.00389749662702329
HEY1#2346244.040111043105710.00375304636917980.0185562850802807
HMGN3#932436.133910792512940.006640696683324720.0282861340556201
MAX#414934.839416631755340.01315737137836840.0465921645605877
MEF2A#4205314.0574231822330.0005830038854186610.00488552858775893
MXI1#460137.471178721569470.003741314738550960.0186225893613346
MYC#460945.22228187160940.001344309395272740.00885626246974638
PAX5#507935.002174148383370.01196533174786410.0434735530497539
SIN3A#2594245.408884726815140.001168172384885160.00794392210606986
SP2#6668213.07676524692230.008330036536614940.0328009910586106
TAF1#687243.343046285745290.008005664898701650.0321269408782133
TAF7#687938.574802053692940.00250055433515240.0140262846666836
TBP#690843.706770687096390.005296377814784350.0243506076157009
TCF7L2#693438.077632422353010.002978381685834620.0158566144103013
TFAP2C#702238.106921457395170.002947011739866440.015714436796687
THAP1#55145215.68457230142570.005840469678357920.0262421619660137
USF1#739146.361499277207960.0006105011399140830.00506998477667676
YY1#752844.911170749853860.00171871838055440.0106617503532146
ZBTB33#10009215.83236251499060.005734248930324640.0258349175632706
ZBTB7A#5134135.513931980906920.009038352821081090.0342248841695692
ZNF143#7702413.50087655222793.00867915035614e-050.000619647883620676



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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