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Coexpression cluster:C202: Difference between revisions

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

Latest revision as of 10:55, 17 September 2013


Full id: C202_salivary_skin_penis_tongue_uterus_cervical_immature



Phase1 CAGE Peaks

Hg19::chr10:134756449..134756462,+p@chr10:134756449..134756462
+
Hg19::chr10:30847379..30847383,-p@chr10:30847379..30847383
-
Hg19::chr10:47740297..47740299,+p1@FAM25HP
Hg19::chr11:34218778..34218792,+p@chr11:34218778..34218792
+
Hg19::chr11:85195171..85195180,+p@chr11:85195171..85195180
+
Hg19::chr11:86285462..86285463,-p@chr11:86285462..86285463
-
Hg19::chr12:110318334..110318354,-p2@GLTP
Hg19::chr12:53070961..53070973,-p@chr12:53070961..53070973
-
Hg19::chr12:53074182..53074197,-p1@KRT1
Hg19::chr12:53171128..53171131,-p1@KRT76
Hg19::chr15:28560796..28560799,+p1@ENST00000544920
Hg19::chr16:70597904..70597915,+p5@SF3B3
Hg19::chr17:38261177..38261211,-p@chr17:38261177..38261211
-
Hg19::chr17:38975796..38975805,-p13@KRT10
Hg19::chr17:38975820..38975830,-p10@KRT10
Hg19::chr17:38975839..38975846,-p14@KRT10
Hg19::chr17:38975850..38975854,-p19@KRT10
Hg19::chr17:38975877..38975899,-p4@KRT10
Hg19::chr17:38975907..38975928,-p3@KRT10
Hg19::chr17:38976407..38976413,-p20@KRT10
Hg19::chr17:38976601..38976615,-p@chr17:38976601..38976615
-
Hg19::chr17:38976637..38976653,-p@chr17:38976637..38976653
-
Hg19::chr17:38976811..38976823,-p@chr17:38976811..38976823
-
Hg19::chr17:38976838..38976861,-p@chr17:38976838..38976861
-
Hg19::chr17:38976882..38976895,-p@chr17:38976882..38976895
-
Hg19::chr17:38976909..38976919,-p@chr17:38976909..38976919
-
Hg19::chr17:38977317..38977333,-p@chr17:38977317..38977333
-
Hg19::chr17:38977346..38977362,-p@chr17:38977346..38977362
-
Hg19::chr17:38977367..38977371,-p@chr17:38977367..38977371
-
Hg19::chr17:38978257..38978272,-p6@KRT10
Hg19::chr17:38978288..38978293,-p21@KRT10
Hg19::chr17:38978422..38978432,-p12@KRT10
Hg19::chr17:38978519..38978529,-p9@KRT10
Hg19::chr17:38978526..38978535,+p@chr17:38978526..38978535
+
Hg19::chr17:38978586..38978620,-p5@KRT10
Hg19::chr17:38978621..38978636,-p8@KRT10
Hg19::chr17:38978676..38978690,-p3@AB590331
Hg19::chr17:38978718..38978740,-p1@AB590331
Hg19::chr17:38978741..38978756,-p2@AB590331
Hg19::chr17:38978856..38978875,-p1@KRT10
Hg19::chr17:995196..995215,-p22@ABR
Hg19::chr18:28742652..28742696,-p1@DSC1
Hg19::chr18:28742704..28742718,-p3@DSC1
Hg19::chr18:28742813..28742824,-p2@DSC1
Hg19::chr19:24006861..24006869,-p@chr19:24006861..24006869
-
Hg19::chr19:35981358..35981374,-p1@KRTDAP
Hg19::chr19:36004543..36004557,-p3@DMKN
Hg19::chr19:39575002..39575011,+p2@PAPL
Hg19::chr19:6333599..6333612,-p1@ACER1
Hg19::chr19:6333614..6333628,-p2@ACER1
Hg19::chr1:152769195..152769200,+p1@LCE1D
Hg19::chr1:152779121..152779133,-p1@LCE1C
Hg19::chr1:152783824..152783828,+p@chr1:152783824..152783828
+
Hg19::chr1:152798501..152798507,+p1@LCE1A
Hg19::chr1:152919679..152919684,+p@chr1:152919679..152919684
+
Hg19::chr1:82165350..82165387,+p7@LPHN2
Hg19::chr20:42647752..42647774,-p@chr20:42647752..42647774
-
Hg19::chr20:43753104..43753107,-p1@WFDC12
Hg19::chr21:45943378..45943388,+p@chr21:45943378..45943388
+
Hg19::chr22:19466467..19466531,-p4@UFD1L
Hg19::chr2:204400013..204400047,-p1@RAPH1
Hg19::chr2:70188755..70188770,-p2@ASPRV1
Hg19::chr3:106617542..106617578,+p1@MTND5P16
Hg19::chr3:72387462..72387488,-p@chr3:72387462..72387488
-
Hg19::chr5:147481380..147481398,+p@chr5:147481380..147481398
+
Hg19::chr5:175837672..175837682,-p@chr5:175837672..175837682
-
Hg19::chr5:67511303..67511333,+p19@PIK3R1
Hg19::chr5:79948121..79948150,-p@chr5:79948121..79948150
-
Hg19::chr5:99385325..99385350,-p@chr5:99385325..99385350
-
Hg19::chr6:24955923..24955927,-p@chr6:24955923..24955927
-
Hg19::chr6:25004678..25004688,-p@chr6:25004678..25004688
-
Hg19::chr6:7578742..7578757,+p@chr6:7578742..7578757
+
Hg19::chr7:7604061..7604072,-p@chr7:7604061..7604072
-
Hg19::chr8:145118330..145118353,-p@chr8:145118330..145118353
-
Hg19::chr8:145118355..145118372,-p@chr8:145118355..145118372
-
Hg19::chr9:115209821..115209831,+p@chr9:115209821..115209831
+
Hg19::chr9:87879610..87879618,+p@chr9:87879610..87879618
+
Hg19::chr9:96698887..96698909,+p@chr9:96698887..96698909
+
Hg19::chrX:114608236..114608237,+p@chrX:114608236..114608237
+


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:0008544epidermis development7.04856330701466e-07
GO:0007398ectoderm development7.04856330701466e-07
GO:0009888tissue development1.85687015891158e-05
GO:0031424keratinization4.38422775379148e-05
GO:0009913epidermal cell differentiation7.63587513186168e-05
GO:0048730epidermis morphogenesis9.04537395326773e-05
GO:0048729tissue morphogenesis0.000175394644674861
GO:0048513organ development0.000260134436990178
GO:0048731system development0.00159417645728387
GO:0005882intermediate filament0.00386161842764485
GO:0045111intermediate filament cytoskeleton0.00386161842764485
GO:0048856anatomical structure development0.00409978112833119
GO:0007275multicellular organismal development0.00796701061421971
GO:0035030phosphoinositide 3-kinase complex, class IA0.008242081714353
GO:0001867complement activation, lectin pathway0.0144204585980542
GO:0043559insulin binding0.0144204585980542
GO:0009653anatomical structure morphogenesis0.017490948924798
GO:0043125ErbB-3 class receptor binding0.025625053188339
GO:0043560insulin receptor substrate binding0.0303387592429232
GO:0032502developmental process0.037338278254163
GO:0048009insulin-like growth factor receptor signaling pathway0.0383951793796147
GO:0005856cytoskeleton0.0383951793796147
GO:0042730fibrinolysis0.0383951793796147
GO:0017046peptide hormone binding0.0383951793796147
GO:0017089glycolipid transporter activity0.0383951793796147
GO:0051861glycolipid binding0.0383951793796147
GO:0035014phosphoinositide 3-kinase regulator activity0.0383951793796147
GO:0046836glycolipid transport0.0397103858141704
GO:0030280structural constituent of epidermis0.0397103858141704
GO:0005159insulin-like growth factor receptor binding0.042216059074444
GO:0030195negative regulation of blood coagulation0.0445584391949209
GO:0032501multicellular organismal process0.0453360829683806
GO:0030193regulation of blood coagulation0.0453360829683806



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><br>

Uber Anatomy
Ontology termp-valuen
saliva-secreting gland7.51e-346
gland of oral region7.51e-346
gland of foregut7.51e-346
oral gland7.51e-346
oral cavity7.51e-346
penis1.67e-231
intromittent organ1.67e-231
lateral plate mesenchyme1.67e-231
undifferentiated genital tubercle1.67e-231
somatopleure1.67e-231
surface2.10e-231
gland of gut1.20e-2010
oral opening1.70e-1622
uterine cervix1.89e-156
neck of organ1.89e-156
mouth1.27e-1229
stomodeum1.27e-1229
orifice3.03e-1036
tongue1.30e-083
gustatory system1.30e-083
future tongue1.30e-083
subdivision of head1.28e-0749
exocrine gland4.21e-0731
exocrine system4.21e-0731
zone of skin7.70e-074


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)
MA0003.10.000721901
MA0004.10.0336197
MA0006.10.000453849
MA0007.10.183148
MA0009.11.39735
MA0014.10.00173636
MA0017.10.575111
MA0019.10.110504
MA0024.10.0929193
MA0025.10.221947
MA0027.11.54322
MA0028.10.0506836
MA0029.10.332498
MA0030.10.318882
MA0031.10.246801
MA0038.10.206973
MA0040.10.339539
MA0041.10.240939
MA0042.10.0875364
MA0043.10.143525
MA0046.10.137621
MA0048.10.00172762
MA0050.10.0295206
MA0051.10.017337
MA0052.10.105802
MA0055.10.000383282
MA0056.10
MA0057.10.0154922
MA0058.10.0904857
MA0059.10.0361108
MA0060.10.000995808
MA0061.10.0572228
MA0063.10
MA0066.11.35037
MA0067.10.351447
MA0068.10.467978
MA0069.10.135616
MA0070.10.129875
MA0071.11.15426
MA0072.10.401085
MA0073.10.0333384
MA0074.10.200729
MA0076.10.0444531
MA0077.10.123747
MA0078.10.148554
MA0081.10.0361844
MA0083.10.147377
MA0084.11.25284
MA0087.11.29153
MA0088.10.0052002
MA0089.10
MA0090.10.0159486
MA0091.10.21522
MA0092.10.295184
MA0093.10.0423459
MA0095.10
MA0098.10
MA0100.11.85783
MA0101.10.0965331
MA0103.10.552644
MA0105.10.0180145
MA0106.10.107788
MA0107.10.0678081
MA0108.23.07772
MA0109.10
MA0111.10.640876
MA0113.10.286168
MA0114.10.19234
MA0115.10.295117
MA0116.10.214578
MA0117.10.492546
MA0119.10.265479
MA0122.10.529087
MA0124.11.3495
MA0125.10.605092
MA0130.10
MA0131.10.163892
MA0132.10
MA0133.10
MA0135.10.15992
MA0136.10.0855174
MA0139.10.387389
MA0140.10.158015
MA0141.10.466355
MA0142.11.72364
MA0143.10.286429
MA0144.10.0928012
MA0145.10.107897
MA0146.11.49466e-05
MA0147.10.0145746
MA0148.10.251608
MA0149.10.0543486
MA0062.20.0045087
MA0035.20.0586137
MA0039.20.000289288
MA0138.20.149567
MA0002.20.0422127
MA0137.20.210848
MA0104.20.0108633
MA0047.20.245403
MA0112.20.301721
MA0065.20.0807479
MA0150.10.0490339
MA0151.10
MA0152.10.32945
MA0153.10.20008
MA0154.10.0163137
MA0155.10.0169961
MA0156.10.347195
MA0157.10.419535
MA0158.10
MA0159.10.484785
MA0160.10.733089
MA0161.10
MA0162.10.000211597
MA0163.17.57189e-07
MA0164.10.128815
MA0080.20.430635
MA0018.20.108751
MA0099.20.33014
MA0079.21.37064e-05
MA0102.20.533076
MA0258.11.22916
MA0259.10.00541663
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
MAFF#2376474.989968296577420.0005260705474545170.00455536704299829
MAFK#797582.744378039273910.008732948823018410.0331803129411823
ZNF263#10127181.873331005901170.005952049741028030.0266929802002416



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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