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Coexpression cluster:C195: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;28:2.89589366263268:1.2138110998422e-07:6.98838023464274e-06!JUN#3725;21:3.02033808090877:3.74013144524048e-06:0.000122334979019565!NR3C1#2908;15:2.58155574675397:0.000617226990610799:0.00511648302820869!SMARCA4#6597;4:7.2076277382937:0.00241060574578793:0.0135903510652818!STAT3#6774;32:3.86922850470041:6.10156636443326e-12:7.85747829266394e-10
|tf_chipseq_enrich=FOS#2353;28:2.89589366263268:1.2138110998422e-07:6.98838023464274e-06!JUN#3725;21:3.02033808090877:3.74013144524048e-06:0.000122334979019565!NR3C1#2908;15:2.58155574675397:0.000617226990610799:0.00511648302820869!SMARCA4#6597;4:7.2076277382937:0.00241060574578793:0.0135903510652818!STAT3#6774;32:3.86922850470041:6.10156636443326e-12:7.85747829266394e-10
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|tfbs_overrepresentation_for_novel_motifs=0.112349,0.000100454,0.0176079,0.0310022,0.646967,1.8439,0.0125961,1.68875,0.101205,0.0537661,0.0220323,2.27057,0.0411862,0.0551818,0.201743,0.257198,0.0630494,0.172479,0.0934602,0.220617,0.0480365,0.00660748,0.0281386,0.111673,0.0330314,0.456896,0.33412,0.330798,0.00215097,0.0490584,0.0170284,0.263808,0.0602628,0.182606,0.0746985,0.198001,0.00412287,0.0308492,0.363428,0.0400852,1.58925,0.0138597,0.152139,0.632023,0.000807433,0.0699651,0.0611129,0.141869,0.267252,0.0637102,0.0252069,0.0142325,0.025369,0.108444,0.553723,0.152528,2.80187,0.0082359,0.0800365,0.0422192,0.0926978,0.013022,0.344825,0.0540099,0.0153943,0.168337,1.26978,0.526182,0.252841,0.393896,0.0116265,0.668264,1.14271e-07,0.55086,6.61724e-05,0.125336,0.0177784,0.183733,0.0712243,2.94403,0.908834,0.0536759,0.185361,0.175875,0.15852,1.47576e-10,0.00226878,0.229411,0.0306037,0.61185,0.309197,0.869931,1.48196,0.411556,0.00204894,0.339685,1.70479,0.330467,0.03163,0.112182,0.511887,0.580255,0.0981973,0.854315,0.363188,0.00352509,0.0589802,0.295884,0.0329275,0.0200943,0.0207828,0.0969993,0.179102,0.0752952,0.275276,1.03522,2.65301e-06,0.241856,0.0432631,0.300751,0.53906,0.123687,0.551109,0.948696,0.355498,0.412514,0.154869,0.0848111,0.208721,0.147969,0.144374,0.132152,0.217709,3.77883,0.8535,0.0592721,0.826275,0.332048,0.288143,1.03171,0.658175,0.725941,0.807541,0.669669,0.0412657,0.0394109,0.339535,0.8809,0.762791,0.00494471,0.0453667,2.88446e-07,0.87233,0.0874229,0.164914,0.418018,0.113855,0.278629,0.0330555,0.0225679,0.724042,0.419958,0.070937,0.230069,0.695614,0.0708668,0.0940388,0.320699,2.74878e-11
}}
}}

Revision as of 13:45, 26 November 2012


Full id: C195_Small_Gingival_Bronchial_Smooth_mesenchymal_Urothelial_Tracheal



Phase1 CAGE Peaks

Hg19::chr10:3941138..3941145,-p@chr10:3941138..3941145
-
Hg19::chr11:127965642..127965659,+p@chr11:127965642..127965659
+
Hg19::chr11:127965706..127965714,+p@chr11:127965706..127965714
+
Hg19::chr11:127965736..127965745,+p@chr11:127965736..127965745
+
Hg19::chr11:127965839..127965844,+p@chr11:127965839..127965844
+
Hg19::chr11:127965855..127965866,+p@chr11:127965855..127965866
+
Hg19::chr11:127965869..127965894,+p@chr11:127965869..127965894
+
Hg19::chr11:127965904..127965913,+p@chr11:127965904..127965913
+
Hg19::chr11:127965924..127965935,+p@chr11:127965924..127965935
+
Hg19::chr11:73663222..73663226,+p@chr11:73663222..73663226
+
Hg19::chr11:7927293..7927308,-p4@LOC283299
Hg19::chr11:7927797..7927817,-p1@LOC283299
Hg19::chr12:10513712..10513716,-p1@ENST00000535911
Hg19::chr12:28186158..28186183,-p@chr12:28186158..28186183
-
Hg19::chr14:51963969..51963974,+p@chr14:51963969..51963974
+
Hg19::chr14:51972517..51972536,+p@chr14:51972517..51972536
+
Hg19::chr14:52026212..52026215,+p@chr14:52026212..52026215
+
Hg19::chr14:87730650..87730656,-p@chr14:87730650..87730656
-
Hg19::chr15:71740021..71740037,+p@chr15:71740021..71740037
+
Hg19::chr16:85750444..85750466,-p@chr16:85750444..85750466
-
Hg19::chr17:38653561..38653607,-p@chr17:38653561..38653607
-
Hg19::chr17:56603082..56603097,+p@chr17:56603082..56603097
+
Hg19::chr17:56603128..56603137,+p@chr17:56603128..56603137
+
Hg19::chr17:60858418..60858439,-p@chr17:60858418..60858439
-
Hg19::chr1:107541218..107541228,-p@chr1:107541218..107541228
-
Hg19::chr1:209591333..209591335,-p@chr1:209591333..209591335
-
Hg19::chr1:232854914..232854917,-p@chr1:232854914..232854917
-
Hg19::chr1:8135925..8135929,-p@chr1:8135925..8135929
-
Hg19::chr1:94160495..94160512,-p@chr1:94160495..94160512
-
Hg19::chr21:38233478..38233483,+p@chr21:38233478..38233483
+
Hg19::chr21:44939980..44939983,+p@chr21:44939980..44939983
+
Hg19::chr2:163101439..163101452,+p@chr2:163101439..163101452
+
Hg19::chr2:213770576..213770587,+p@chr2:213770576..213770587
+
Hg19::chr2:231649545..231649550,-p@chr2:231649545..231649550
-
Hg19::chr2:56007040..56007060,+p@chr2:56007040..56007060
+
Hg19::chr2:73299315..73299328,-p11@SFXN5
Hg19::chr3:101909113..101909129,+p@chr3:101909113..101909129
+
Hg19::chr3:101909187..101909198,+p@chr3:101909187..101909198
+
Hg19::chr3:156502182..156502186,+p@chr3:156502182..156502186
+
Hg19::chr3:189655696..189655699,+p@chr3:189655696..189655699
+
Hg19::chr3:45476797..45476808,+p@chr3:45476797..45476808
+
Hg19::chr3:45476828..45476831,+p@chr3:45476828..45476831
+
Hg19::chr3:45476837..45476843,+p@chr3:45476837..45476843
+
Hg19::chr3:48602467..48602469,-p14@COL7A1
Hg19::chr4:108783895..108783898,-p@chr4:108783895..108783898
-
Hg19::chr4:108909370..108909373,+p@chr4:108909370..108909373
+
Hg19::chr4:157695866..157695871,+p@chr4:157695866..157695871
+
Hg19::chr4:166604070..166604073,+p@chr4:166604070..166604073
+
Hg19::chr5:111445067..111445085,-p@chr5:111445067..111445085
-
Hg19::chr5:148293809..148293816,+p@chr5:148293809..148293816
+
Hg19::chr5:52584337..52584344,-p@chr5:52584337..52584344
-
Hg19::chr5:59064137..59064148,-p58@PDE4D
Hg19::chr5:59064162..59064173,-p72@PDE4D
Hg19::chr5:59064199..59064230,-p28@PDE4D
Hg19::chr6:10355646..10355663,-p@chr6:10355646..10355663
-
Hg19::chr6:11791877..11791883,+p@chr6:11791877..11791883
+
Hg19::chr6:12324677..12324683,+p@chr6:12324677..12324683
+
Hg19::chr6:128922463..128922497,+p@chr6:128922463..128922497
+
Hg19::chr6:22222867..22222878,-p@chr6:22222867..22222878
-
Hg19::chr7:106060323..106060328,-p@chr7:106060323..106060328
-
Hg19::chr7:134328418..134328421,+p@chr7:134328418..134328421
+
Hg19::chr7:158196067..158196075,-p@chr7:158196067..158196075
-
Hg19::chr7:55163202..55163244,+p@chr7:55163202..55163244
+
Hg19::chr7:55263885..55263894,+p@chr7:55263885..55263894
+
Hg19::chr8:113686674..113686685,-p@chr8:113686674..113686685
-
Hg19::chr8:113686693..113686717,-p@chr8:113686693..113686717
-
Hg19::chr8:113686738..113686743,-p@chr8:113686738..113686743
-
Hg19::chr8:113686752..113686753,-p@chr8:113686752..113686753
-
Hg19::chr8:113686755..113686782,-p@chr8:113686755..113686782
-
Hg19::chr8:113686792..113686795,-p@chr8:113686792..113686795
-
Hg19::chr8:29414184..29414190,+p@chr8:29414184..29414190
+
Hg19::chr8:29448825..29448836,-p@chr8:29448825..29448836
-
Hg19::chr8:29449835..29449837,+p@chr8:29449835..29449837
+
Hg19::chr9:20224892..20224905,-p@chr9:20224892..20224905
-
Hg19::chr9:21468453..21468457,-p@chr9:21468453..21468457
-
Hg19::chr9:21499276..21499289,-p@chr9:21499276..21499289
-
Hg19::chr9:21499446..21499456,-p@chr9:21499446..21499456
-
Hg19::chr9:21505384..21505411,-p@chr9:21505384..21505411
-
Hg19::chr9:21543873..21543886,-p@chr9:21543873..21543886
-
Hg19::chr9:21549553..21549570,-p@chr9:21549553..21549570
-
Hg19::chr9:21549612..21549619,-p@chr9:21549612..21549619
-
Hg19::chr9:21559689..21559703,-p3@MIR31HG
Hg19::chr9:21559717..21559731,-p4@MIR31HG
Hg19::chr9:21559788..21559806,-p2@MIR31HG
Hg19::chr9:21559809..21559877,-p1@MIR31HG
Hg19::chrX:48369279..48369286,+p9@PORCN
Hg19::chrY:7671916..7671924,-p@chrY:7671916..7671924
-


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:0005590collagen type VII0.0114211703756034
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0342514094620916
GO:0030934anchoring collagen0.0342514094620916
GO:0005737cytoplasm0.0456463678366286
GO:0005626insoluble fraction0.0456463678366286



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
gingival epithelium1.49e-403
mouth mucosa1.26e-1613
epithelium of mucosa1.16e-158
gingiva1.16e-158
jaw skeleton2.95e-144
splanchnocranium2.95e-144
primary subdivision of cranial skeletal system1.35e-115
mucosa6.57e-1120
respiratory system8.01e-1174
endoderm-derived structure1.66e-10160
endoderm1.66e-10160
presumptive endoderm1.66e-10160
protuberance8.11e-106
pharyngeal arch8.11e-106
embryonic head8.11e-106
orifice3.42e-0936
head3.08e-0856
surface structure8.74e-0899
mouth1.36e-0729
stomodeum1.36e-0729
anterior region of body2.09e-0762
craniocervical region2.09e-0762


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
FOS#2353282.895893662632681.2138110998422e-076.98838023464274e-06
JUN#3725213.020338080908773.74013144524048e-060.000122334979019565
NR3C1#2908152.581555746753970.0006172269906107990.00511648302820869
SMARCA4#659747.20762773829370.002410605745787930.0135903510652818
STAT3#6774323.869228504700416.10156636443326e-127.85747829266394e-10



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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