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{{Coexpression_clusters
{
|full_id=C321_synovial_anaplastic_maxillary_glassy_keratoacanthoma_rhabdomyosarcoma_small
|

Latest revision as of 11:20, 17 September 2013


Full id: C321_synovial_anaplastic_maxillary_glassy_keratoacanthoma_rhabdomyosarcoma_small



Phase1 CAGE Peaks

Hg19::chr10:135140510..135140524,-p@chr10:135140510..135140524
-
Hg19::chr11:21774394..21774400,-p@chr11:21774394..21774400
-
Hg19::chr12:130529575..130529613,-p1@ENST00000538806
Hg19::chr12:130529670..130529676,-p2@ENST00000538806
Hg19::chr12:130646534..130646542,+p5@FZD10
Hg19::chr12:130646999..130647019,+p1@FZD10
Hg19::chr12:130647116..130647131,+p2@FZD10
Hg19::chr12:130647145..130647153,+p3@FZD10
Hg19::chr12:130786785..130786827,-p@chr12:130786785..130786827
-
Hg19::chr12:54348655..54348693,+p1@HOXC12
Hg19::chr12:54348702..54348715,+p2@HOXC12
Hg19::chr12:54379011..54379016,+p15@HOXC10
Hg19::chr12:54379029..54379057,+p2@HOXC10
Hg19::chr12:54379066..54379073,+p11@HOXC10
Hg19::chr12:54384370..54384382,+p5@HOXC6
Hg19::chr12:91435143..91435151,-p@chr12:91435143..91435151
-
Hg19::chr15:68117826..68117829,+p9@SKOR1
Hg19::chr15:68117872..68117879,+p6@SKOR1
Hg19::chr15:68118244..68118272,+p@chr15:68118244..68118272
+
Hg19::chr15:68124311..68124318,+p@chr15:68124311..68124318
+
Hg19::chr15:68124344..68124357,+p@chr15:68124344..68124357
+
Hg19::chr15:68124362..68124376,+p@chr15:68124362..68124376
+
Hg19::chr1:172134667..172134711,+p@chr1:172134667..172134711
+
Hg19::chr1:172134736..172134739,+p@chr1:172134736..172134739
+
Hg19::chr1:172134755..172134764,+p@chr1:172134755..172134764
+
Hg19::chr1:172134783..172134793,+p@chr1:172134783..172134793
+
Hg19::chr1:219718163..219718176,+p@chr1:219718163..219718176
+
Hg19::chr22:26149439..26149448,+p@chr22:26149439..26149448
+
Hg19::chr2:176964515..176964540,+p1@HOXD12
Hg19::chr2:181556734..181556740,+p@chr2:181556734..181556740
+
Hg19::chr2:181751144..181751146,+p@chr2:181751144..181751146
+
Hg19::chr4:101716139..101716140,+p@chr4:101716139..101716140
+
Hg19::chr4:139010162..139010169,+p1@LOC641364
Hg19::chr4:139010187..139010202,+p1@uc003ihi.1
Hg19::chr8:37411632..37411639,-p1@ENST00000517363
Hg19::chr8:37411648..37411657,-p1@ENST00000519738


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:0007275multicellular organismal development8.65863811875033e-05
GO:0043565sequence-specific DNA binding8.65863811875033e-05
GO:0032502developmental process0.000253043555760244
GO:0032501multicellular organismal process0.000298748618863444
GO:0003700transcription factor activity0.000298748618863444
GO:0006355regulation of transcription, DNA-dependent0.00464369786151737
GO:0006351transcription, DNA-dependent0.00464369786151737
GO:0032774RNA biosynthetic process0.00464369786151737
GO:0003677DNA binding0.00464369786151737
GO:0045449regulation of transcription0.00464369786151737
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00464369786151737
GO:0006350transcription0.00464369786151737
GO:0010468regulation of gene expression0.00464369786151737
GO:0031323regulation of cellular metabolic process0.00476772728591122
GO:0019907cyclin-dependent protein kinase activating kinase holoenzyme complex0.00482608410494648
GO:0019222regulation of metabolic process0.00486300595795212
GO:0016070RNA metabolic process0.00486300595795212
GO:0042813Wnt receptor activity0.00536168429154834
GO:0004926non-G-protein coupled 7TM receptor activity0.00952012014547746
GO:0010467gene expression0.0118595404623073
GO:0050794regulation of cellular process0.0134218833994459
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0141002922494947
GO:0005634nucleus0.0154428728835454
GO:0050789regulation of biological process0.015582156017373
GO:0003676nucleic acid binding0.0172927417511276
GO:0065007biological regulation0.0204372947530772
GO:0044428nuclear part0.0302271088318504
GO:0043283biopolymer metabolic process0.0355069171746445
GO:0000228nuclear chromosome0.0409632259144425
GO:0003714transcription corepressor activity0.0427774530679075
GO:0043231intracellular membrane-bound organelle0.0462403008804392
GO:0043227membrane-bound organelle0.0462403008804392



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
synovial cell2.39e-663
GAG secreting cell2.62e-239
carbohydrate secreting cell2.62e-239
extracellular matrix secreting cell1.22e-1415
stromal cell1.52e-0828
secretory cell5.81e-0736
Uber Anatomy
Ontology termp-valuen
stratified squamous epithelium2.39e-663
layer of synovial tissue2.39e-663
synovial joint2.39e-663
synovial membrane of synovial joint2.39e-663
articulation5.22e-268
skeletal joint5.22e-268
articular system5.22e-268
cavity lining6.76e-1812
serous membrane6.76e-1812
squamous epithelium2.15e-0925
Disease
Ontology termp-valuen
sarcoma2.29e-1120


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)
MA0003.12.07069
MA0004.10.512856
MA0006.10.0866247
MA0007.10.0601181
MA0009.10.357426
MA0014.10.681865
MA0017.10.0281901
MA0019.10.139271
MA0024.10.760558
MA0025.10.466941
MA0027.11.88112
MA0028.10.0227941
MA0029.10.291715
MA0030.10.283226
MA0031.10.667192
MA0038.11.21665
MA0040.10.29608
MA0041.10.0750477
MA0042.10.223255
MA0043.10.357676
MA0046.10.348837
MA0048.12.08812
MA0050.10.0624764
MA0051.10.112588
MA0052.10.298977
MA0055.10.232975
MA0056.10
MA0057.13.52921
MA0058.10.591929
MA0059.10.0344842
MA0060.12.06874
MA0061.10.231212
MA0063.10
MA0066.10.368427
MA0067.10.628098
MA0068.12.05798
MA0069.10.34581
MA0070.10.337064
MA0071.10.0954724
MA0072.10.333568
MA0073.110.0314
MA0074.10.73024
MA0076.10.0394639
MA0077.10.873791
MA0078.10.168619
MA0081.10.13844
MA0083.10.363385
MA0084.10.800231
MA0087.10.331671
MA0088.10.755273
MA0089.10
MA0090.10.679811
MA0091.10.51837
MA0092.10.199374
MA0093.10.426307
MA0095.10
MA0098.10
MA0100.10.386851
MA0101.10.228124
MA0103.10.204359
MA0105.10.400534
MA0106.10.13708
MA0107.10.452852
MA0108.20.23485
MA0109.10
MA0111.12.64494
MA0113.10.448878
MA0114.10.00824813
MA0115.10.560015
MA0116.10.268902
MA0117.10.387522
MA0119.10.0301744
MA0122.10.408619
MA0124.10.523698
MA0125.10.451839
MA0130.10
MA0131.10.179874
MA0132.10
MA0133.10
MA0135.10.381677
MA0136.11.24072
MA0139.11.3069
MA0140.10.313174
MA0141.10.583356
MA0142.11.15789
MA0143.11.41669
MA0144.11.20581
MA0145.10.875316
MA0146.10.257173
MA0147.10.1348
MA0148.10.077765
MA0149.10.0896745
MA0062.20.047645
MA0035.20.644966
MA0039.22.8482
MA0138.22.21642
MA0002.20.0635913
MA0137.20.476948
MA0104.20.163409
MA0047.20.130332
MA0112.20.330707
MA0065.20.100539
MA0150.10.0420855
MA0151.10
MA0152.10.321644
MA0153.10.43772
MA0154.10.0911204
MA0155.10.124231
MA0156.10.105502
MA0157.10.573093
MA0158.10
MA0159.10.277818
MA0160.10.0844683
MA0161.10
MA0162.10.77275
MA0163.10.286168
MA0164.10.153683
MA0080.21.02675
MA0018.20.843597
MA0099.20.0975183
MA0079.210.2626
MA0102.20.835136
MA0258.10.0058251
MA0259.10.294872
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
SUZ12#23512811.13684020245844.58523204098634e-072.17276338080114e-05



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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