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Coexpression cluster:C160: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!5.15e-42!115;UBERON:0005743!5.43e-37!86;UBERON:0001017!1.91e-34!82;UBERON:0000073!4.65e-34!94;UBERON:0001016!4.65e-34!94;UBERON:0001049!1.20e-31!57;UBERON:0005068!1.20e-31!57;UBERON:0006241!1.20e-31!57;UBERON:0007135!1.20e-31!57;UBERON:0002346!9.21e-31!90;UBERON:0003075!1.76e-30!86;UBERON:0007284!1.76e-30!86;UBERON:0000955!1.68e-29!69;UBERON:0006238!1.68e-29!69;UBERON:0002616!9.13e-28!59;UBERON:0000924!1.23e-27!173;UBERON:0006601!1.23e-27!173;UBERON:0004121!4.63e-27!169;UBERON:0000033!7.02e-25!123;UBERON:0000153!7.97e-25!129;UBERON:0007811!7.97e-25!129;UBERON:0003056!5.46e-24!61;UBERON:0002780!1.03e-23!41;UBERON:0001890!1.03e-23!41;UBERON:0006240!1.03e-23!41;UBERON:0003080!1.48e-23!42;UBERON:0002020!2.28e-19!34;UBERON:0003528!2.28e-19!34;UBERON:0001893!2.28e-19!34;UBERON:0002791!8.07e-19!33;UBERON:0001869!4.39e-18!32;UBERON:0000062!1.03e-17!511;UBERON:0000475!1.75e-16!365;UBERON:0000481!1.87e-16!347;UBERON:0000956!2.90e-14!25;UBERON:0000203!2.90e-14!25;UBERON:0000468!7.32e-14!659;UBERON:0002619!7.44e-14!22;UBERON:0000064!1.02e-13!219;UBERON:0001950!1.34e-12!20;UBERON:0000483!2.86e-11!309;UBERON:0000119!3.04e-11!312;UBERON:0000467!4.21e-11!625;UBERON:0000480!7.50e-11!626;UBERON:0000922!8.52e-11!612;UBERON:0004111!2.04e-10!241;UBERON:0000025!4.47e-10!194;UBERON:0000477!1.05e-09!286;UBERON:0003076!3.69e-09!15;UBERON:0003057!3.69e-09!15;UBERON:0002050!5.37e-09!605;UBERON:0005423!5.37e-09!605;UBERON:0000923!9.66e-09!604;UBERON:0005291!9.66e-09!604;UBERON:0006598!9.66e-09!604;UBERON:0002532!9.66e-09!604;UBERON:0004732!6.53e-08!13;UBERON:0004733!2.29e-07!12;UBERON:0002028!2.29e-07!12;UBERON:0007277!2.29e-07!12;UBERON:0005177!3.90e-07!107
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}}
}}

Revision as of 17:28, 8 August 2012


Full id: C160_medulla_Hepatocyte_retina_corpus_liver_pineal_cerebral



Phase1 CAGE Peaks

Hg19::chr10:18240814..18240829,+p5@SLC39A12
Hg19::chr10:18240834..18240897,+p1@SLC39A12
Hg19::chr10:18242109..18242116,+p9@SLC39A12
Hg19::chr10:18242120..18242136,+p4@SLC39A12
Hg19::chr10:18242141..18242184,+p2@SLC39A12
Hg19::chr11:119216846..119216857,-p@chr11:119216846..119216857
-
Hg19::chr11:119217365..119217398,-p1@MFRP
p2@C1QTNF5
Hg19::chr11:62783276..62783295,-p2@SLC22A8
Hg19::chr11:71869850..71869861,+p1@ENST00000544535
Hg19::chr11:71900740..71900772,+p3@FOLR1
Hg19::chr12:129304411..129304414,-p11@SLC15A4
Hg19::chr12:20951599..20951604,+p@chr12:20951599..20951604
+
Hg19::chr12:44467399..44467407,+p12@TMEM117
Hg19::chr12:44467410..44467418,+p13@TMEM117
Hg19::chr12:47779637..47779662,-p@chr12:47779637..47779662
-
Hg19::chr14:91932629..91932652,-p14@SMEK1
Hg19::chr15:40492238..40492270,+p8@BUB1B
Hg19::chr15:68924373..68924411,+p16@CORO2B
Hg19::chr17:48912918..48912925,+p3@WFIKKN2
Hg19::chr17:48912939..48912963,+p1@WFIKKN2
Hg19::chr17:48913037..48913055,+p2@WFIKKN2
Hg19::chr17:48913092..48913105,+p4@WFIKKN2
Hg19::chr17:57229155..57229198,-p@chr17:57229155..57229198
-
Hg19::chr18:29171832..29171847,+p1@TTR
Hg19::chr18:29172846..29172875,+p4@TTR
Hg19::chr18:29172879..29172882,+p5@TTR
Hg19::chr18:29172884..29172921,+p2@TTR
Hg19::chr18:29172924..29172962,+p3@TTR
Hg19::chr18:29175078..29175088,+p@chr18:29175078..29175088
+
Hg19::chr18:29175095..29175110,+p@chr18:29175095..29175110
+
Hg19::chr18:29175113..29175118,+p@chr18:29175113..29175118
+
Hg19::chr18:29175123..29175131,+p@chr18:29175123..29175131
+
Hg19::chr18:29175152..29175199,+p@chr18:29175152..29175199
+
Hg19::chr18:29175184..29175198,-p@chr18:29175184..29175198
-
Hg19::chr18:29178527..29178571,+p@chr18:29178527..29178571
+
Hg19::chr18:29178550..29178583,-p@chr18:29178550..29178583
-
Hg19::chr18:29178574..29178579,+p@chr18:29178574..29178579
+
Hg19::chr18:29178581..29178599,+p@chr18:29178581..29178599
+
Hg19::chr18:29178596..29178626,-p@chr18:29178596..29178626
-
Hg19::chr18:29178609..29178620,+p@chr18:29178609..29178620
+
Hg19::chr18:29178630..29178652,-p@chr18:29178630..29178652
-
Hg19::chr18:29178636..29178652,+p@chr18:29178636..29178652
+
Hg19::chr18:29178674..29178686,-p@chr18:29178674..29178686
-
Hg19::chr18:29178674..29178693,+p@chr18:29178674..29178693
+
Hg19::chr18:29178704..29178717,+p@chr18:29178704..29178717
+
Hg19::chr18:29178720..29178749,+p@chr18:29178720..29178749
+
Hg19::chr18:59423008..59423021,+p@chr18:59423008..59423021
+
Hg19::chr19:16830652..16830663,+p3@NWD1
Hg19::chr19:16830713..16830741,+p4@NWD1
Hg19::chr19:16830774..16830814,+p1@NWD1
Hg19::chr1:20617362..20617380,+p1@VWA5B1
Hg19::chr1:220924670..220924672,+p@chr1:220924670..220924672
+
Hg19::chr20:30264810..30264831,-p@chr20:30264810..30264831
-
Hg19::chr21:25014751..25014755,+p@chr21:25014751..25014755
+
Hg19::chr2:62453859..62453863,-p@chr2:62453859..62453863
-
Hg19::chr2:8851401..8851408,+p@chr2:8851401..8851408
+
Hg19::chr3:156840776..156840823,-p1@LOC339894
Hg19::chr3:193096512..193096519,-p3@ATP13A5
Hg19::chr3:193096536..193096547,-p1@ATP13A5
Hg19::chr3:59750150..59750155,-p@chr3:59750150..59750155
-
Hg19::chr3:59750161..59750179,-p@chr3:59750161..59750179
-
Hg19::chr3:59750186..59750202,-p@chr3:59750186..59750202
-
Hg19::chr3:59750207..59750262,-p@chr3:59750207..59750262
-
Hg19::chr3:61241825..61241830,-p@chr3:61241825..61241830
-
Hg19::chr4:186318393..186318446,-p@chr4:186318393..186318446
-
Hg19::chr4:34621389..34621413,+p@chr4:34621389..34621413
+
Hg19::chr5:33514132..33514156,+p@chr5:33514132..33514156
+
Hg19::chr5:35089799..35089804,-p20@PRLR
Hg19::chr5:35089832..35089839,-p26@PRLR
Hg19::chr5:35089843..35089860,-p7@PRLR
Hg19::chr5:35089867..35089884,-p5@PRLR
Hg19::chr5:35090057..35090065,-p27@PRLR
Hg19::chr5:35090259..35090267,-p12@PRLR
Hg19::chr5:35090318..35090324,-p@chr5:35090318..35090324
-
Hg19::chr6:132580699..132580702,+p@chr6:132580699..132580702
+
Hg19::chr7:129012882..129012891,-p@chr7:129012882..129012891
-
Hg19::chr7:129013106..129013120,-p@chr7:129013106..129013120
-
Hg19::chr7:129015511..129015519,+p30@AHCYL2
Hg19::chr7:129015540..129015550,+p23@AHCYL2
Hg19::chr7:129015616..129015619,+p38@AHCYL2
Hg19::chr7:129015671..129015685,+p11@AHCYL2
Hg19::chr7:129015806..129015815,+p@chr7:129015806..129015815
+
Hg19::chr7:129015906..129015915,+p@chr7:129015906..129015915
+
Hg19::chr7:129027894..129027906,+p16@AHCYL2
Hg19::chr7:135366185..135366192,-p@chr7:135366185..135366192
-
Hg19::chr7:135366210..135366222,-p@chr7:135366210..135366222
-
Hg19::chr7:135366373..135366382,-p@chr7:135366373..135366382
-
Hg19::chr7:135412540..135412552,-p2@SLC13A4
Hg19::chr7:135412925..135412944,-p1@SLC13A4
Hg19::chr7:150529074..150529076,+p@chr7:150529074..150529076
+
Hg19::chr7:151771377..151771389,+p2@GALNT11
Hg19::chr7:151772200..151772217,+p13@GALNT11
Hg19::chr7:80255485..80255507,+p24@CD36
Hg19::chr7:80255514..80255524,+p28@CD36
Hg19::chr8:120685906..120685920,-p4@ENPP2
Hg19::chr8:12803139..12803144,+p23@KIAA1456
Hg19::chr8:12803146..12803155,+p17@KIAA1456
Hg19::chr8:12803176..12803195,+p3@KIAA1456
Hg19::chr8:72234691..72234696,-p13@EYA1
Hg19::chr9:113490531..113490547,+p@chr9:113490531..113490547
+
Hg19::chr9:130637244..130637303,-p4@AK1
Hg19::chr9:20927844..20927855,+p@chr9:20927844..20927855
+
Hg19::chr9:34381453..34381479,-p3@C9orf24
Hg19::chr9:5954514..5954521,-p18@KIAA2026
Hg19::chr9:73396238..73396243,-p@chr9:73396238..73396243
-
Hg19::chrX:106163626..106163638,+p2@CLDN2
Hg19::chrX:108041633..108041636,+p@chrX:108041633..108041636
+
Hg19::chrX:109683362..109683372,-p9@AMMECR1
Hg19::chrX:152798683..152798691,+p@chrX:152798683..152798691
+


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:0016021integral to membrane0.0111405358355432
GO:0031224intrinsic to membrane0.0111405358355432
GO:0016020membrane0.0130779249451524
GO:0044425membrane part0.0130779249451524
GO:0015382sodium:sulfate symporter activity0.02254798068998
GO:0004925prolactin receptor activity0.02254798068998
GO:0046655folic acid metabolic process0.02254798068998
GO:0042976activation of JAK protein0.02254798068998
GO:0042977tyrosine phosphorylation of JAK2 protein0.02254798068998
GO:0047391alkylglycerophosphoethanolamine phosphodiesterase activity0.02254798068998
GO:0042978ornithine decarboxylase activator activity0.02254798068998
GO:0051179localization0.0370790960593757
GO:0015349thyroid hormone transmembrane transporter activity0.0370790960593757
GO:0005887integral to plasma membrane0.0370790960593757
GO:0031226intrinsic to plasma membrane0.0370790960593757
GO:0007171transmembrane receptor protein tyrosine kinase activation (dimerization)0.0413124155449544
GO:0000940outer kinetochore of condensed chromosome0.0413124155449544
GO:0051233spindle midzone0.0413124155449544
GO:0004528phosphodiesterase I activity0.0490975201158827
GO:0044459plasma membrane part0.0490975201158827
GO:0006810transport0.0490975201158827



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.15e-42115
central nervous system1.91e-3482
regional part of nervous system4.65e-3494
nervous system4.65e-3494
neural tube1.20e-3157
neural rod1.20e-3157
future spinal cord1.20e-3157
neural keel1.20e-3157
neurectoderm9.21e-3190
neural plate1.76e-3086
presumptive neural plate1.76e-3086
brain1.68e-2969
future brain1.68e-2969
regional part of brain9.13e-2859
ectoderm1.23e-27173
presumptive ectoderm1.23e-27173
ectoderm-derived structure4.63e-27169
head7.02e-25123
anterior region of body7.97e-25129
craniocervical region7.97e-25129
pre-chordal neural plate5.46e-2461
regional part of forebrain1.03e-2341
forebrain1.03e-2341
future forebrain1.03e-2341
anterior neural tube1.48e-2342
gray matter2.28e-1934
brain grey matter2.28e-1934
telencephalon2.28e-1934
regional part of telencephalon8.07e-1933
cerebral hemisphere4.39e-1832
organ1.03e-17511
organism subdivision1.75e-16365
multi-tissue structure1.87e-16347
cerebral cortex2.90e-1425
pallium2.90e-1425
multi-cellular organism7.32e-14659
regional part of cerebral cortex7.44e-1422
organ part1.02e-13219
neocortex1.34e-1220
epithelium2.86e-11309
cell layer3.04e-11312
anatomical system4.21e-11625
anatomical group7.50e-11626
embryo8.52e-11612
anatomical conduit2.04e-10241
tube4.47e-10194
anatomical cluster1.05e-09286
posterior neural tube3.69e-0915
chordal neural plate3.69e-0915
embryonic structure5.37e-09605
developing anatomical structure5.37e-09605
germ layer9.66e-09604
embryonic tissue9.66e-09604
presumptive structure9.66e-09604
epiblast (generic)9.66e-09604
segmental subdivision of nervous system6.53e-0813
segmental subdivision of hindbrain2.29e-0712
hindbrain2.29e-0712
presumptive hindbrain2.29e-0712
trunk region element3.90e-07107


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

No analysis results for this cluster

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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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