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{{Coexpression_clusters
{
|full_id=C398_neuroepithelioma_neuroectodermal_carcinoid_neuroblastoma_spinal_brain_synovial
 

Latest revision as of 11:22, 17 September 2013


Full id: C398_neuroepithelioma_neuroectodermal_carcinoid_neuroblastoma_spinal_brain_synovial



Phase1 CAGE Peaks

Hg19::chr10:29717478..29717509,-p@chr10:29717478..29717509
-
Hg19::chr11:121097296..121097326,+p@chr11:121097296..121097326
+
Hg19::chr11:68611721..68611749,-p@chr11:68611721..68611749
-
Hg19::chr13:100953150..100953169,+p@chr13:100953150..100953169
+
Hg19::chr18:61034757..61034768,-p5@KDSR
Hg19::chr19:31840130..31840160,-p2@TSHZ3
Hg19::chr19:49915463..49915468,+p@chr19:49915463..49915468
+
Hg19::chr19:49950830..49950836,-p@chr19:49950830..49950836
-
Hg19::chr1:18958059..18958081,+p6@PAX7
Hg19::chr1:22696471..22696505,-p@chr1:22696471..22696505
-
Hg19::chr1:37499838..37499850,-p3@GRIK3
Hg19::chr20:21494684..21494708,-p1@NKX2-2
Hg19::chr2:162137741..162137745,+p@chr2:162137741..162137745
+
Hg19::chr5:147011027..147011032,-p@chr5:147011027..147011032
-
Hg19::chr5:147011039..147011055,-p@chr5:147011039..147011055
-
Hg19::chr5:147011082..147011102,-p@chr5:147011082..147011102
-
Hg19::chr6:50786057..50786069,+p9@TFAP2B
Hg19::chr7:121943677..121943690,+p1@LOC154860
Hg19::chr8:12808791..12808798,+p28@KIAA1456
Hg19::chr8:12809246..12809265,+p6@KIAA1456
Hg19::chr8:1922789..1922822,-p1@ENST00000521498
Hg19::chr8:37554297..37554313,+p@chr8:37554297..37554313
+
Hg19::chr8:37824101..37824132,-p1@ADRB3
Hg19::chr8:37824176..37824185,-p4@ADRB3
Hg19::chr8:37824442..37824447,-p9@ADRB3
Hg19::chrX:51361761..51361770,-p2@ENST00000417339


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:0043565sequence-specific DNA binding0.00116055591153121
GO:0003700transcription factor activity0.00493005322372769
GO:0015052beta3-adrenergic receptor activity0.00825679971741433
GO:0021529spinal cord oligodendrocyte cell differentiation0.00825679971741433
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.00875366199758637
GO:0007275multicellular organismal development0.00875366199758637
GO:0051380norepinephrine binding0.00880530874965199
GO:0048522positive regulation of cellular process0.00880530874965199
GO:0045817positive regulation of global transcription from RNA polymerase II promoter0.00880530874965199
GO:0048518positive regulation of biological process0.00880530874965199
GO:0045893positive regulation of transcription, DNA-dependent0.00880530874965199
GO:0050794regulation of cellular process0.00880530874965199
GO:0006358regulation of global transcription from RNA polymerase II promoter0.00880530874965199
GO:0048665neuron fate specification0.00880530874965199
GO:0004939beta-adrenergic receptor activity0.00880530874965199
GO:0050789regulation of biological process0.00939786051904262
GO:0045941positive regulation of transcription0.00939786051904262
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00939786051904262
GO:0021515cell differentiation in spinal cord0.00939786051904262
GO:0031018endocrine pancreas development0.00939786051904262
GO:0032502developmental process0.00939786051904262
GO:0006355regulation of transcription, DNA-dependent0.00939786051904262
GO:0006351transcription, DNA-dependent0.00939786051904262
GO:0032774RNA biosynthetic process0.00939786051904262
GO:0014003oligodendrocyte development0.00939786051904262
GO:0015277kainate selective glutamate receptor activity0.00939786051904262
GO:0043410positive regulation of MAPKKK cascade0.00939786051904262
GO:0003677DNA binding0.00939786051904262
GO:0065007biological regulation0.00939786051904262
GO:0045449regulation of transcription0.00939786051904262
GO:0031325positive regulation of cellular metabolic process0.00939786051904262
GO:0046983protein dimerization activity0.00939786051904262
GO:0031016pancreas development0.00939786051904262
GO:0021510spinal cord development0.00939786051904262
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00939786051904262
GO:0009893positive regulation of metabolic process0.00939786051904262
GO:0048709oligodendrocyte differentiation0.00939786051904262
GO:0006350transcription0.00939786051904262
GO:0032501multicellular organismal process0.00939786051904262
GO:0010468regulation of gene expression0.00939786051904262
GO:0031323regulation of cellular metabolic process0.00997615312025724
GO:0006357regulation of transcription from RNA polymerase II promoter0.00997615312025724
GO:0021782glial cell development0.00997615312025724
GO:0048663neuron fate commitment0.0104193052793127
GO:0043408regulation of MAPKKK cascade0.0104193052793127
GO:0001708cell fate specification0.0104193052793127
GO:0004935adrenoceptor activity0.0104193052793127
GO:0019222regulation of metabolic process0.0104193052793127
GO:0016070RNA metabolic process0.0104193052793127
GO:0048856anatomical structure development0.0134138326126212
GO:0007215glutamate signaling pathway0.0135794335084424
GO:0007190adenylate cyclase activation0.0145845525423315
GO:0045762positive regulation of adenylate cyclase activity0.0153058715131997
GO:0031281positive regulation of cyclase activity0.0153058715131997
GO:0051349positive regulation of lyase activity0.0153058715131997
GO:0042562hormone binding0.0153058715131997
GO:0006366transcription from RNA polymerase II promoter0.0164796078645652
GO:0010001glial cell differentiation0.0164796078645652
GO:0035270endocrine system development0.0184293903317657
GO:0007399nervous system development0.0190433330980239
GO:0001822kidney development0.0190433330980239
GO:0042063gliogenesis0.0190433330980239
GO:0004970ionotropic glutamate receptor activity0.0190433330980239
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0190433330980239
GO:0005234extracellular-glutamate-gated ion channel activity0.0197609833425238
GO:0001655urogenital system development0.0199591205669183
GO:0045761regulation of adenylate cyclase activity0.0200429495925894
GO:0031279regulation of cyclase activity0.0200429495925894
GO:0051339regulation of lyase activity0.0200429495925894
GO:0010467gene expression0.0202245390867495
GO:0043176amine binding0.0204028976861871
GO:0045597positive regulation of cell differentiation0.0214865664443413
GO:0006112energy reserve metabolic process0.0247581429427409
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0247581429427409
GO:0005634nucleus0.0278121819963144
GO:0008227amine receptor activity0.0289750242419746
GO:0051094positive regulation of developmental process0.0290234365138574
GO:0045165cell fate commitment0.0299087690292912
GO:0005231excitatory extracellular ligand-gated ion channel activity0.029943891968136
GO:0003676nucleic acid binding0.0314626919076973
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0340418938006602
GO:0019933cAMP-mediated signaling0.0348107586320543
GO:0048513organ development0.0348107586320543
GO:0008066glutamate receptor activity0.0364148977951553
GO:0043170macromolecule metabolic process0.0364148977951553
GO:0048468cell development0.0394914210203462
GO:0043235receptor complex0.0414249758746352
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0429729248948776
GO:0015980energy derivation by oxidation of organic compounds0.0429729248948776
GO:0005887integral to plasma membrane0.0429729248948776
GO:0031226intrinsic to plasma membrane0.0434087731362005
GO:0019935cyclic-nucleotide-mediated signaling0.0434087731362005
GO:0005230extracellular ligand-gated ion channel activity0.0460793535836692
GO:0007420brain development0.0483447649736714
GO:0045595regulation of cell differentiation0.0493591462687715
GO:0042165neurotransmitter binding0.0493591462687715



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
sympathetic nervous system1.28e-235
autonomic nervous system1.28e-235
neural tissue1.15e-152
peripheral nervous system1.31e-138


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)
MA0003.10.381689
MA0004.10.122847
MA0006.10.180714
MA0007.10.112494
MA0009.10.46676
MA0014.10.439973
MA0017.10.49094
MA0019.10.619765
MA0024.10.378349
MA0025.10.584598
MA0027.12.02165
MA0028.10.198989
MA0029.10.394311
MA0030.10.384823
MA0031.10.33249
MA0038.10.186009
MA0040.10.399176
MA0041.10.824723
MA0042.10.74466
MA0043.10.467032
MA0046.10.457379
MA0048.10.217815
MA0050.10.115873
MA0051.10.539526
MA0052.10.402401
MA0055.10.172598
MA0056.10
MA0057.10.342135
MA0058.10.0742284
MA0059.10.0736469
MA0060.10.184491
MA0061.10.497568
MA0063.10
MA0066.10.186292
MA0067.10.753856
MA0068.10.202094
MA0069.10.454067
MA0070.10.44448
MA0071.10.160989
MA0072.10.44064
MA0073.11.48063
MA0074.10.182721
MA0076.10.0815705
MA0077.10.434073
MA0078.10.252504
MA0081.10.256536
MA0083.11.1922
MA0084.10.931415
MA0087.10.438554
MA0088.11.91036
MA0089.10
MA0090.10.088522
MA0091.10.784572
MA0092.10.103692
MA0093.10.184116
MA0095.10
MA0098.10
MA0100.10.568627
MA0101.10.41897
MA0103.10.0445972
MA0105.12.21141
MA0106.10.61335
MA0107.10.505179
MA0108.20.330055
MA0109.10
MA0111.10.0952636
MA0113.10.225587
MA0114.10.107626
MA0115.10.682809
MA0116.10.515572
MA0117.10.499451
MA0119.10.0665855
MA0122.10.522217
MA0124.10.644657
MA0125.10.568516
MA0130.10
MA0131.10.26595
MA0132.10
MA0133.10
MA0135.12.13819
MA0136.10.557618
MA0139.10.125994
MA0140.10.15932
MA0141.10.254116
MA0142.10.307468
MA0143.10.225712
MA0144.11.06812
MA0145.10.468357
MA0146.10.177975
MA0147.10.118663
MA0148.10.137223
MA0149.1114.502
MA0062.20.277944
MA0035.20.158878
MA0039.20.713264
MA0138.20.705339
MA0002.20.166167
MA0137.20.789967
MA0104.20.0703325
MA0047.20.205658
MA0112.21.07124
MA0065.20.0514803
MA0150.10.0856547
MA0151.10
MA0152.10.491228
MA0153.11.363
MA0154.10.641878
MA0155.10.00039491
MA0156.10.797544
MA0157.10.286356
MA0158.10
MA0159.10.528033
MA0160.10.448616
MA0161.10
MA0162.10.413129
MA0163.10.173916
MA0164.10.23445
MA0080.20.41213
MA0018.20.215022
MA0099.20.16368
MA0079.23.19911
MA0102.20.967149
MA0258.11.01611
MA0259.10.300465
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
MAFF#2376436.497925748839830.01072147509855170.0395751798196663



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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