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{{Coexpression_clusters
{
|full_id=C160_medulla_Hepatocyte_retina_corpus_liver_pineal_cerebral
 

Latest revision as of 10:45, 17 September 2013


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
medulla oblongata5.53e-473
myelencephalon5.53e-473
future myelencephalon5.53e-473
pineal body2.97e-312
regional part of epithalamus2.97e-312
secretory circumventricular organ2.97e-312
circumventricular organ2.97e-312
epithalamus2.97e-312
brainstem6.70e-246
regional part of nervous system3.36e-2253
regional part of brain3.36e-2253
central nervous system2.67e-2181
neural tube5.38e-2156
neural rod5.38e-2156
future spinal cord5.38e-2156
neural keel5.38e-2156
brain6.26e-2168
future brain6.26e-2168
diencephalon4.19e-207
future diencephalon4.19e-207
nervous system4.00e-1989
adult organism2.81e-18114
neural plate1.44e-1782
presumptive neural plate1.44e-1782
corpus callosum6.47e-171
central nervous system cell part cluster6.47e-171
axon tract6.47e-171
intercerebral commissure6.47e-171
dorsal telencephalic commissure6.47e-171
brain white matter6.47e-171
brain commissure6.47e-171
white matter6.47e-171
nervous system commissure6.47e-171
cerebral hemisphere white matter6.47e-171
neurectoderm1.02e-1686
gland of diencephalon3.59e-164
neuroendocrine gland3.59e-164
regional part of diencephalon3.59e-164
ecto-epithelium1.07e-13104
regional part of forebrain7.30e-1341
forebrain7.30e-1341
anterior neural tube7.30e-1341
future forebrain7.30e-1341
segmental subdivision of hindbrain2.75e-1212
hindbrain2.75e-1212
presumptive hindbrain2.75e-1212
pre-chordal neural plate1.25e-1161
ectoderm-derived structure1.34e-11171
ectoderm1.34e-11171
presumptive ectoderm1.34e-11171
segmental subdivision of nervous system2.18e-1113
structure with developmental contribution from neural crest1.30e-10132
posterior neural tube6.02e-1015
chordal neural plate6.02e-1015
multi cell component structure4.02e-092
neuron projection bundle4.02e-092
Ammon's horn4.34e-092
lobe parts of cerebral cortex4.34e-092
hippocampal formation4.34e-092
limbic lobe4.34e-092
meninx4.70e-092
membrane organ4.70e-092
meningeal cluster4.70e-092
organ system subdivision4.22e-07223


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)
MA0003.10
MA0004.10.622109
MA0006.10.000350575
MA0007.10.0628276
MA0009.10.99599
MA0014.11.68757e-14
MA0017.11.33027
MA0019.11.33452
MA0024.10.0472324
MA0025.11.40267
MA0027.11.4058
MA0028.10.263846
MA0029.10.195976
MA0030.12.09886
MA0031.10.31224
MA0038.10.191031
MA0040.10.444381
MA0041.10.699697
MA0042.10.78678
MA0043.10.0829567
MA0046.11.98555
MA0048.10.00061681
MA0050.10.138903
MA0051.11.07441
MA0052.10.204999
MA0055.12.6433e-05
MA0056.10
MA0057.10.00104939
MA0058.10.793304
MA0059.10.422406
MA0060.10.0022266
MA0061.10.068905
MA0063.10
MA0066.10.345076
MA0067.10.2546
MA0068.10.000409944
MA0069.10.266146
MA0070.10.541654
MA0071.11.20349
MA0072.11.89136
MA0073.10
MA0074.10.0278332
MA0076.10.888839
MA0077.10.518838
MA0078.10.347839
MA0081.10.0217941
MA0083.10.085822
MA0084.11.79253
MA0087.13.1017
MA0088.10.00129186
MA0089.10
MA0090.11.53187
MA0091.10.0315262
MA0092.10.325403
MA0093.10.813612
MA0095.10
MA0098.10
MA0100.10.00618941
MA0101.10.0873721
MA0103.10.194522
MA0105.12.67547e-07
MA0106.10.00838611
MA0107.10.0225395
MA0108.20.563137
MA0109.10
MA0111.10.00375161
MA0113.10.00994759
MA0114.10.492633
MA0115.11.12013
MA0116.10.00127264
MA0117.10.098373
MA0119.10.0837553
MA0122.10.719742
MA0124.10.180752
MA0125.10.831298
MA0130.10
MA0131.10.0167544
MA0132.10
MA0133.10
MA0135.17.70679
MA0136.10.0929953
MA0139.10.0803143
MA0140.10.0599637
MA0141.10.281385
MA0142.13.72768
MA0143.11.40447
MA0144.10.144918
MA0145.10.0245848
MA0146.15.43672e-08
MA0147.10.0263385
MA0148.11.97328
MA0149.10.0544238
MA0062.20.0358478
MA0035.20.257809
MA0039.20
MA0138.20.0144107
MA0002.20.294604
MA0137.20.109827
MA0104.20.0127855
MA0047.21.24792
MA0112.20.0273611
MA0065.20.000158328
MA0150.10.0110998
MA0151.10
MA0152.10.271835
MA0153.13.25155
MA0154.10.110769
MA0155.10.000107996
MA0156.10.188917
MA0157.10.438272
MA0158.10
MA0159.10.00144198
MA0160.10.114653
MA0161.10
MA0162.12.33849e-14
MA0163.14.41986e-09
MA0164.10.302268
MA0080.20.00710514
MA0018.20.123028
MA0099.20.0202533
MA0079.20
MA0102.21.07704
MA0258.10.184176
MA0259.10.00180952
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
POU5F1#5460412.3096954661250.0003393076685397590.00344985918950778



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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