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Coexpression cluster:C1109: Difference between revisions

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|tf_chipseq_enrich=STAT3#6774;4:6.01112285551671:0.00225577915639448:0.0128101418799784
|tf_chipseq_enrich=STAT3#6774;4:6.01112285551671:0.00225577915639448:0.0128101418799784
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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.247072,0.384703,0.529489,0.343148,0.52784,0.604235,0.643217,0.224331,0.0544999,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,0.19568,0.0986842,1.00032,0.23059,0.520063,0.338096,0.430372,0.670692,0.164928,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.186138,0.309012,0.232776,0.305874,0.529001,1.4117,0.207499,0.307642,0.459366,0.541549,0.340293,0.0257952,0.415364,0.60533,0.486696,0.0670664,0.346342,0.684981,0.617179,0.117127,0.941629,1.09491,0.595623,1.65331,0.562713,0.150585,0.561701,0.905643,0.60771,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,0.850825,1.0864,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.322252,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,0.132387,0.776034,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,1.45665,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,1.4603,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,1.46724,0.00626991
}}
}}

Revision as of 14:41, 26 November 2012


Full id: C1109_Urothelial_Small_Gingival_Mallassezderived_Prostate_Sebocyte_Bronchial



Phase1 CAGE Peaks

Hg19::chr10:127763979..127763984,+p@chr10:127763979..127763984
+
Hg19::chr12:28125953..28125964,-p17@PTHLH
Hg19::chr12:28125967..28125978,-p16@PTHLH
Hg19::chr1:116048147..116048169,+p@chr1:116048147..116048169
+
Hg19::chr1:165873233..165873247,+p6@UCK2
Hg19::chr6:151358048..151358060,+p13@MTHFD1L
Hg19::chr8:141728760..141728771,-p36@PTK2


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:0004849uridine kinase activity0.0336539626688756
GO:0004329formate-tetrahydrofolate ligase activity0.0336539626688756
GO:0019206nucleoside kinase activity0.0336539626688756
GO:0007172signal complex assembly0.0336539626688756
GO:0005524ATP binding0.0336539626688756
GO:0042169SH2 domain binding0.0336539626688756
GO:0032559adenyl ribonucleotide binding0.0336539626688756
GO:0030554adenyl nucleotide binding0.0336539626688756
GO:0007595lactation0.0336539626688756
GO:0046058cAMP metabolic process0.0336539626688756
GO:0005925focal adhesion0.0336539626688756
GO:0032553ribonucleotide binding0.0336539626688756
GO:0032555purine ribonucleotide binding0.0336539626688756
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0336539626688756
GO:0005924cell-substrate adherens junction0.0336539626688756
GO:0009396folic acid and derivative biosynthetic process0.0336539626688756
GO:0017076purine nucleotide binding0.0336539626688756
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0336539626688756
GO:0030055cell-matrix junction0.0336539626688756
GO:0006760folic acid and derivative metabolic process0.035162178684034
GO:0009187cyclic nucleotide metabolic process0.0380442230049447
GO:0005912adherens junction0.0389687822508273
GO:0000166nucleotide binding0.0389687822508273
GO:0048609reproductive process in a multicellular organism0.0389687822508273
GO:0032504multicellular organism reproduction0.0389687822508273
GO:0043623cellular protein complex assembly0.042369104863588
GO:0007565female pregnancy0.0433708075059849
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0433708075059849
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0433708075059849
GO:0016323basolateral plasma membrane0.0433708075059849
GO:0007229integrin-mediated signaling pathway0.0433708075059849
GO:0019933cAMP-mediated signaling0.0433708075059849
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0439824022570293



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>

Cell Type
Ontology termp-valuen
respiratory epithelial cell7.19e-3413
endo-epithelial cell1.91e-3042
transitional epithelial cell2.40e-304
urothelial cell2.40e-304
general ecto-epithelial cell1.28e-2414
epithelial cell of Malassez5.63e-233
gingival epithelial cell5.01e-223
endodermal cell2.50e-2158
epithelial cell8.09e-18253
sebum secreting cell1.80e-152
epithelial cell of sweat gland1.80e-152
epithelial cell of skin gland1.80e-152
acinar cell of sebaceous gland1.80e-152
epidermal cell6.42e-139
epithelial cell of tracheobronchial tree7.27e-139
epithelial cell of lower respiratory tract7.27e-139
stratified squamous epithelial cell3.65e-116
keratin accumulating cell3.65e-116
stratified epithelial cell3.65e-116
keratinizing barrier epithelial cell3.65e-116
epithelial fate stem cell3.65e-116
stratified epithelial stem cell3.65e-116
surface ectodermal cell3.65e-116
bronchial epithelial cell1.55e-103
duct epithelial cell2.27e-103
branched duct epithelial cell2.27e-103
tracheal epithelial cell2.27e-103
tracheoblast2.27e-103
ecto-epithelial cell1.15e-0934
epithelial cell of alimentary canal1.02e-0820
embryonic cell1.40e-08250
buccal mucosa cell2.13e-081
endothelial cell of viscerocranial mucosa2.13e-081
keratinized cell of the oral mucosa2.13e-081
epithelial cell of esophagus2.46e-081
bladder cell4.07e-081
lower urinary tract cell4.07e-081
mammary gland epithelial cell8.57e-084
Uber Anatomy
Ontology termp-valuen
urothelium1.07e-365
transitional epithelium1.42e-306
gingival epithelium5.01e-223
jaw skeleton2.20e-174
splanchnocranium2.20e-174
skin gland1.80e-152
epidermis gland1.80e-152
gland of integumental system1.80e-152
sebaceous gland1.80e-152
skin sebaceous gland1.80e-152
sweat gland1.80e-152
sweat gland placode1.80e-152
sebaceous gland placode1.80e-152
epithelium of mucosa2.51e-148
primary subdivision of cranial skeletal system5.11e-145
endoderm-derived structure1.92e-12160
endoderm1.92e-12160
presumptive endoderm1.92e-12160
protuberance9.09e-126
pharyngeal arch9.09e-126
embryonic head9.09e-126
lower respiratory tract epithelium1.55e-103
epithelium of bronchus1.55e-103
surface structure8.31e-1099
respiratory system1.05e-0974
mouth mucosa5.80e-0913
endo-epithelium9.35e-0982
mucosa1.15e-0820
gingiva1.34e-088
urinary bladder urothelium4.07e-081
wall of urinary bladder4.07e-081
mucosa of urinary bladder4.07e-081
skin epidermis8.30e-0815
outer epithelium8.30e-0815
enveloping layer of ectoderm8.30e-0815
mammary gland8.57e-084
mammary bud8.57e-084
mammary ridge8.57e-084
mammary placode8.57e-084
tracheobronchial tree8.92e-0815
lower respiratory tract8.92e-0815
respiratory tract2.44e-0754


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#promotersEnrichmentp-valueq-value
STAT3#677446.011122855516710.002255779156394480.0128101418799784



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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