Coexpression cluster:C321

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 ID	GO name	FDR corrected p-value
GO:0007275	multicellular organismal development	8.65863811875033e-05
GO:0043565	sequence-specific DNA binding	8.65863811875033e-05
GO:0032502	developmental process	0.000253043555760244
GO:0032501	multicellular organismal process	0.000298748618863444
GO:0003700	transcription factor activity	0.000298748618863444
GO:0006355	regulation of transcription, DNA-dependent	0.00464369786151737
GO:0006351	transcription, DNA-dependent	0.00464369786151737
GO:0032774	RNA biosynthetic process	0.00464369786151737
GO:0003677	DNA binding	0.00464369786151737
GO:0045449	regulation of transcription	0.00464369786151737
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00464369786151737
GO:0006350	transcription	0.00464369786151737
GO:0010468	regulation of gene expression	0.00464369786151737
GO:0031323	regulation of cellular metabolic process	0.00476772728591122
GO:0019907	cyclin-dependent protein kinase activating kinase holoenzyme complex	0.00482608410494648
GO:0019222	regulation of metabolic process	0.00486300595795212
GO:0016070	RNA metabolic process	0.00486300595795212
GO:0042813	Wnt receptor activity	0.00536168429154834
GO:0004926	non-G-protein coupled 7TM receptor activity	0.00952012014547746
GO:0010467	gene expression	0.0118595404623073
GO:0050794	regulation of cellular process	0.0134218833994459
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0141002922494947
GO:0005634	nucleus	0.0154428728835454
GO:0050789	regulation of biological process	0.015582156017373
GO:0003676	nucleic acid binding	0.0172927417511276
GO:0065007	biological regulation	0.0204372947530772
GO:0044428	nuclear part	0.0302271088318504
GO:0043283	biopolymer metabolic process	0.0355069171746445
GO:0000228	nuclear chromosome	0.0409632259144425
GO:0003714	transcription corepressor activity	0.0427774530679075
GO:0043231	intracellular membrane-bound organelle	0.0462403008804392
GO:0043227	membrane-bound organelle	0.0462403008804392

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 term	p-value	n
synovial cell	2.39e-66	3
GAG secreting cell	2.62e-23	9
carbohydrate secreting cell	2.62e-23	9
extracellular matrix secreting cell	1.22e-14	15
stromal cell	1.52e-08	28
secretory cell	5.81e-07	36

Uber Anatomy

Ontology term	p-value	n
stratified squamous epithelium	2.39e-66	3
layer of synovial tissue	2.39e-66	3
synovial joint	2.39e-66	3
synovial membrane of synovial joint	2.39e-66	3
articulation	5.22e-26	8
skeletal joint	5.22e-26	8
articular system	5.22e-26	8
cavity lining	6.76e-18	12
serous membrane	6.76e-18	12
squamous epithelium	2.15e-09	25

Disease

Ontology term	p-value	n
sarcoma	2.29e-11	20

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)
{{{tfbs_overrepresentation_jaspar}}}

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	#promoters	Enrichment	p-value	q-value
SUZ12#23512	8	11.1368402024584	4.58523204098634e-07	2.17276338080114e-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.