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Coexpression cluster:C268: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:10, 17 September 2013


Full id: C268_Mallassezderived_Urothelial_Gingival_Small_Bronchial_Tracheal_Prostate



Phase1 CAGE Peaks

Hg19::chr12:28125659..28125672,-p1@PTHLH
Hg19::chr14:51955987..51955996,+p31@FRMD6
Hg19::chr14:51956090..51956101,+p32@FRMD6
Hg19::chr18:26736784..26736799,+p@chr18:26736784..26736799
+
Hg19::chr18:26736800..26736811,+p@chr18:26736800..26736811
+
Hg19::chr18:26736814..26736831,+p@chr18:26736814..26736831
+
Hg19::chr18:67715323..67715368,-p2@RTTN
Hg19::chr1:183155389..183155406,+p1@LAMC2
Hg19::chr1:183189986..183190012,+p@chr1:183189986..183190012
+
Hg19::chr1:183192299..183192310,+p@chr1:183192299..183192310
+
Hg19::chr1:183192330..183192349,+p@chr1:183192330..183192349
+
Hg19::chr1:183195929..183195945,+p@chr1:183195929..183195945
+
Hg19::chr1:183196792..183196807,+p@chr1:183196792..183196807
+
Hg19::chr1:183197647..183197676,+p@chr1:183197647..183197676
+
Hg19::chr1:183201372..183201407,+p@chr1:183201372..183201407
+
Hg19::chr1:183203526..183203539,+p@chr1:183203526..183203539
+
Hg19::chr1:183204745..183204775,+p@chr1:183204745..183204775
+
Hg19::chr1:183204785..183204796,+p@chr1:183204785..183204796
+
Hg19::chr1:183204800..183204830,+p@chr1:183204800..183204830
+
Hg19::chr1:183204832..183204840,+p@chr1:183204832..183204840
+
Hg19::chr1:183205642..183205677,+p@chr1:183205642..183205677
+
Hg19::chr1:183205712..183205723,+p@chr1:183205712..183205723
+
Hg19::chr1:183206514..183206566,+p@chr1:183206514..183206566
+
Hg19::chr1:183206565..183206612,-p@chr1:183206565..183206612
-
Hg19::chr1:183206616..183206643,-p@chr1:183206616..183206643
-
Hg19::chr1:183207431..183207488,+p@chr1:183207431..183207488
+
Hg19::chr1:183207499..183207519,+p@chr1:183207499..183207519
+
Hg19::chr1:183208494..183208511,+p9@LAMC2
Hg19::chr1:183208516..183208541,+p6@LAMC2
Hg19::chr1:183208540..183208573,-p@chr1:183208540..183208573
-
Hg19::chr1:183208543..183208558,+p8@LAMC2
Hg19::chr1:183208607..183208635,+p4@LAMC2
Hg19::chr1:183208643..183208654,+p10@LAMC2
Hg19::chr1:183208657..183208675,+p3@LAMC2
Hg19::chr1:183209165..183209207,+p@chr1:183209165..183209207
+
Hg19::chr1:183209229..183209250,+p@chr1:183209229..183209250
+
Hg19::chr1:183209265..183209312,-p@chr1:183209265..183209312
-
Hg19::chr1:183209335..183209346,-p@chr1:183209335..183209346
-
Hg19::chr1:183211988..183211991,+p@chr1:183211988..183211991
+
Hg19::chr1:183212294..183212340,+p2@LAMC2
Hg19::chr1:183212409..183212419,+p12@LAMC2
Hg19::chr1:183212478..183212492,+p7@LAMC2
Hg19::chr1:183212689..183212705,+p@chr1:183212689..183212705
+
Hg19::chr1:183212941..183212952,+p@chr1:183212941..183212952
+
Hg19::chr1:183212991..183213014,+p@chr1:183212991..183213014
+
Hg19::chr1:183213130..183213176,+p@chr1:183213130..183213176
+
Hg19::chr1:209790842..209790854,-p@chr1:209790842..209790854
-
Hg19::chr1:209826169..209826182,-p4@LAMB3
Hg19::chr3:184018352..184018374,+p3@PSMD2


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

p.valueFDRnGenesnPathwayName
0.0001304200680977750.0256875006414391285ECM-receptor interaction (KEGG):04512
0.0003192428343812150.03368011902721822133Toxoplasmosis (KEGG):05145
0.0002029028486685550.02568750064143912106Amoebiasis (KEGG):05146
0.0001304200680977750.0256875006414391285Small cell lung cancer (KEGG):05222
8.58329659590162e-050.0256875006414391269Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244
0.0001699032356318450.0256875006414391297Cell junction organization (Reactome):REACT_20676



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:0005610laminin-5 complex2.23558022420707e-06
GO:0008544epidermis development3.68581257411776e-05
GO:0007398ectoderm development3.68581257411776e-05
GO:0043256laminin complex3.68581257411776e-05
GO:0009888tissue development0.000241622122118908
GO:0005605basal lamina0.00028975954818347
GO:0005604basement membrane0.000857750512404879
GO:0044420extracellular matrix part0.00235550148606838
GO:0007275multicellular organismal development0.00268383219890349
GO:0044421extracellular region part0.00310151907770258
GO:0048513organ development0.00547554905699508
GO:0032502developmental process0.00858513447901359
GO:0048731system development0.0119522547386036
GO:0032501multicellular organismal process0.0119522547386036
GO:0005838proteasome regulatory particle (sensu Eukaryota)0.0119522547386036
GO:0005578proteinaceous extracellular matrix0.0119522547386036
GO:0048856anatomical structure development0.0175600804050097
GO:0007595lactation0.0175600804050097
GO:0046058cAMP metabolic process0.0175600804050097
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0280252688159154
GO:0009187cyclic nucleotide metabolic process0.036034072684621
GO:0043234protein complex0.0366964549910522
GO:0048609reproductive process in a multicellular organism0.0366964549910522
GO:0032504multicellular organism reproduction0.0366964549910522
GO:0022610biological adhesion0.0366964549910522
GO:0007155cell adhesion0.0366964549910522
GO:0000502proteasome complex (sensu Eukaryota)0.0410003388770995
GO:0008201heparin binding0.0410003388770995
GO:0007565female pregnancy0.042175394935033
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0422702018209267
GO:0019933cAMP-mediated signaling0.0423582494144555



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
endo-epithelial cell2.47e-3642
epithelial cell8.98e-36253
respiratory epithelial cell1.75e-2513
endodermal cell2.41e-2458
general ecto-epithelial cell1.38e-1914
epithelial cell of alimentary canal1.86e-1720
epithelial cell of tracheobronchial tree6.62e-159
epithelial cell of lower respiratory tract6.62e-159
transitional epithelial cell5.28e-134
urothelial cell5.28e-134
squamous epithelial cell3.93e-1263
ecto-epithelial cell1.60e-1134
gingival epithelial cell5.15e-103
epithelial cell of Malassez5.31e-103
bronchial epithelial cell1.69e-093
duct epithelial cell2.01e-093
branched duct epithelial cell2.01e-093
tracheal epithelial cell2.01e-093
tracheoblast2.01e-093
acinar cell3.00e-095
embryonic cell1.40e-08250
stratified squamous epithelial cell2.77e-086
keratin accumulating cell2.77e-086
stratified epithelial cell2.77e-086
keratinizing barrier epithelial cell2.77e-086
epithelial fate stem cell2.77e-086
stratified epithelial stem cell2.77e-086
surface ectodermal cell2.77e-086
epidermal cell3.34e-089
protein secreting cell1.05e-076
mammary gland epithelial cell3.05e-074
animal cell3.90e-07679
eukaryotic cell3.90e-07679
sebum secreting cell5.08e-072
epithelial cell of sweat gland5.08e-072
epithelial cell of skin gland5.08e-072
acinar cell of sebaceous gland5.08e-072
Uber Anatomy
Ontology termp-valuen
urothelium5.19e-155
endoderm-derived structure3.06e-14160
endoderm3.06e-14160
presumptive endoderm3.06e-14160
mouth mucosa1.10e-1213
respiratory system1.23e-1274
transitional epithelium1.94e-126
mucosa of oral region1.27e-104
respiratory system mucosa1.27e-104
gingival epithelium5.15e-103
mucosa1.25e-0920
lower respiratory tract epithelium1.69e-093
epithelium of bronchus1.69e-093
surface structure2.66e-0999
endo-epithelium1.13e-0882
extraembryonic membrane1.56e-0814
membranous layer1.56e-0814
oral opening1.56e-0822
tracheobronchial tree1.72e-0815
lower respiratory tract1.72e-0815
orifice1.77e-0836
head8.52e-0856
mouth1.29e-0729
stomodeum1.29e-0729
jaw skeleton1.41e-074
splanchnocranium1.41e-074
digestive system1.62e-07145
digestive tract1.62e-07145
primitive gut1.62e-07145
mammary gland3.05e-074
mammary bud3.05e-074
mammary ridge3.05e-074
mammary placode3.05e-074
epithelial fold3.16e-0747
respiratory tract4.69e-0754
skin gland5.08e-072
epidermis gland5.08e-072
gland of integumental system5.08e-072
sebaceous gland5.08e-072
skin sebaceous gland5.08e-072
sweat gland5.08e-072
sweat gland placode5.08e-072
sebaceous gland placode5.08e-072
epithelial bud5.65e-0737
organ component layer9.22e-0766
Disease
Ontology termp-valuen
squamous cell carcinoma1.29e-1614


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)
MA0003.17.57608e-10
MA0004.10.13061
MA0006.10.0983993
MA0007.10.0276832
MA0009.10.263756
MA0014.17.26712e-08
MA0017.10.487315
MA0019.10.27961
MA0024.10.193834
MA0025.10.3631
MA0027.11.74826
MA0028.10.114237
MA0029.10.206098
MA0030.10.198787
MA0031.10.481779
MA0038.10.0640272
MA0040.10.209871
MA0041.10.339523
MA0042.10.119762
MA0043.10.263979
MA0046.10.256123
MA0048.10.111458
MA0050.10.846275
MA0051.12.33194
MA0052.10.21238
MA0055.10.727155
MA0056.10
MA0057.10.0270169
MA0058.10.169448
MA0059.10.333736
MA0060.10.000762356
MA0061.10.0813473
MA0063.10
MA0066.10.229222
MA0067.10.514146
MA0068.10.151529
MA0069.11.3029
MA0070.10.245703
MA0071.10.188714
MA0072.10.24262
MA0073.10.000175291
MA0074.10.485229
MA0076.10.015898
MA0077.10.237364
MA0078.10.694373
MA0081.10.168037
MA0083.10.269067
MA0084.10.679402
MA0087.10.240948
MA0088.10.000414391
MA0089.10
MA0090.10.983613
MA0091.10.571065
MA0092.10.103168
MA0093.10.101296
MA0095.10
MA0098.10
MA0100.10.0692891
MA0101.10.104492
MA0103.10.556533
MA0105.10.00250154
MA0106.10.977503
MA0107.10.0137079
MA0108.20.157861
MA0109.10
MA0111.10.0208127
MA0113.10.294463
MA0114.10.202063
MA0115.10.449785
MA0116.10.368435
MA0117.10.790723
MA0119.10.0547027
MA0122.10.309767
MA0124.10.415762
MA0125.10.349207
MA0130.10
MA0131.10.113217
MA0132.10
MA0133.10
MA0135.10.778782
MA0136.10.0666752
MA0139.10.0665841
MA0140.10.0496659
MA0141.10.165669
MA0142.10.141688
MA0143.10.0874172
MA0144.10.00148066
MA0145.10.00247165
MA0146.17.02402e-07
MA0147.10.0503967
MA0148.10.152029
MA0149.10.0465992
MA0062.20.0330991
MA0035.20.414369
MA0039.27.02966e-07
MA0138.20.697089
MA0002.20.102327
MA0137.20.00830828
MA0104.20.0055454
MA0047.20.0753218
MA0112.20.202285
MA0065.20.108507
MA0150.10.957488
MA0151.10
MA0152.11.14934
MA0153.10.336269
MA0154.10.118798
MA0155.10.0721669
MA0156.10.0439403
MA0157.10.126996
MA0158.10
MA0159.10.0508076
MA0160.10.377269
MA0161.10
MA0162.11.18632e-06
MA0163.13.18582e-06
MA0164.11.06792
MA0080.20.101379
MA0018.20.0809015
MA0099.22.72442
MA0079.29.64327e-16
MA0102.20.713248
MA0258.10.620968
MA0259.10.0172555
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

No analysis results for this cluster

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

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