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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 14:18, 17 September 2013


Full id: C4709_Osteoblast_anaplastic_neuroblastoma_gastric_osteosarcoma_small_temporal



Phase1 CAGE Peaks

Hg19::chr7:96635329..96635357,+p9@DLX6
Hg19::chr7:96651945..96651968,-p@chr7:96651945..96651968
-
Hg19::chr7:96654015..96654018,-p3@DLX5


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:0030326embryonic limb morphogenesis1.67356575388897e-05
GO:0035113embryonic appendage morphogenesis1.67356575388897e-05
GO:0048736appendage development1.67356575388897e-05
GO:0060173limb development1.67356575388897e-05
GO:0035107appendage morphogenesis1.67356575388897e-05
GO:0035108limb morphogenesis1.67356575388897e-05
GO:0048598embryonic morphogenesis9.21430411214545e-05
GO:0001501skeletal development0.000409646680478949
GO:0009790embryonic development0.000460607511543315
GO:0045669positive regulation of osteoblast differentiation0.00256078176098444
GO:0007399nervous system development0.00350845721558526
GO:0045667regulation of osteoblast differentiation0.00426765549395418
GO:0043565sequence-specific DNA binding0.00440434259482924
GO:0009653anatomical structure morphogenesis0.0058971223235539
GO:0048513organ development0.00653715891505568
GO:0001649osteoblast differentiation0.0080000871954273
GO:0042472inner ear morphogenesis0.00813161387655096
GO:0042471ear morphogenesis0.0088170948994528
GO:0003700transcription factor activity0.00890942448432714
GO:0048731system development0.00926308952311787
GO:0048839inner ear development0.00926308952311787
GO:0043583ear development0.00977220537817819
GO:0045597positive regulation of cell differentiation0.0104593336467374
GO:0048856anatomical structure development0.0126209096667435
GO:0051094positive regulation of developmental process0.0139177346613956
GO:0007275multicellular organismal development0.0153181195105723
GO:0007423sensory organ development0.0155223093697608
GO:0031214biomineral formation0.0155223093697608
GO:0001503ossification0.0155223093697608
GO:0046849bone remodeling0.0163670509123034
GO:0048771tissue remodeling0.0173216973689242
GO:0007409axonogenesis0.0180455087640718
GO:0048667neuron morphogenesis during differentiation0.0180455087640718
GO:0048812neurite morphogenesis0.0180455087640718
GO:0000904cellular morphogenesis during differentiation0.0184047906051062
GO:0031175neurite development0.019169112608058
GO:0045595regulation of cell differentiation0.0198917898403947
GO:0048666neuron development0.0207102889155031
GO:0032502developmental process0.0212452500808942
GO:0006355regulation of transcription, DNA-dependent0.0212452500808942
GO:0006351transcription, DNA-dependent0.0212833840104711
GO:0032774RNA biosynthetic process0.0212833840104711
GO:0003677DNA binding0.0212936828766488
GO:0045449regulation of transcription0.0212936828766488
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0212936828766488
GO:0032990cell part morphogenesis0.0212936828766488
GO:0030030cell projection organization and biogenesis0.0212936828766488
GO:0048858cell projection morphogenesis0.0212936828766488
GO:0030182neuron differentiation0.0212936828766488
GO:0006350transcription0.0212936828766488
GO:0032501multicellular organismal process0.0212936828766488
GO:0010468regulation of gene expression0.0212936828766488
GO:0031323regulation of cellular metabolic process0.0219963890198013
GO:0050793regulation of developmental process0.0223070232679849
GO:0048699generation of neurons0.0224562671377371
GO:0019222regulation of metabolic process0.022827190887131
GO:0016070RNA metabolic process0.022827190887131
GO:0022008neurogenesis0.0230478209014503
GO:0009888tissue development0.0263589672780351
GO:0009887organ morphogenesis0.0307377263448293
GO:0010467gene expression0.0367545070308573
GO:0000902cell morphogenesis0.0383171077563499
GO:0032989cellular structure morphogenesis0.0383171077563499
GO:0050794regulation of cellular process0.0383171077563499
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0396567305998326
GO:0005634nucleus0.0419114525788757
GO:0050789regulation of biological process0.0424112436476964
GO:0003676nucleic acid binding0.0450760257742571
GO:0065007biological regulation0.049492041671133



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
osteoblast1.52e-1911
osteoprogenitor cell1.52e-1911
mesenchyme condensation cell1.52e-1911
single fate stem cell1.10e-1220
neuronal stem cell4.39e-078
Uber Anatomy
Ontology termp-valuen
cerebral hemisphere6.07e-2732
telencephalon3.87e-2534
regional part of telencephalon6.97e-2432
regional part of forebrain1.47e-2241
forebrain1.47e-2241
anterior neural tube1.47e-2241
future forebrain1.47e-2241
brain grey matter2.85e-2234
gray matter2.85e-2234
nervous system1.43e-1889
central nervous system1.10e-1781
telencephalic nucleus1.15e-167
regional part of nervous system1.76e-1653
regional part of brain1.76e-1653
neural tube2.30e-1556
neural rod2.30e-1556
future spinal cord2.30e-1556
neural keel2.30e-1556
regional part of cerebral cortex2.64e-1422
corpus striatum7.58e-144
striatum7.58e-144
ventral part of telencephalon7.58e-144
future corpus striatum7.58e-144
pre-chordal neural plate9.49e-1461
neocortex3.89e-1320
brain4.27e-1368
future brain4.27e-1368
basal ganglion8.33e-139
neural nucleus8.33e-139
nuclear complex of neuraxis8.33e-139
nucleus of brain8.33e-139
aggregate regional part of brain8.33e-139
collection of basal ganglia8.33e-139
cerebral subcortex8.33e-139
cerebral cortex2.18e-1225
pallium2.18e-1225
caudate-putamen6.71e-113
dorsal striatum6.71e-113
ectoderm-derived structure6.23e-10171
ectoderm6.23e-10171
presumptive ectoderm6.23e-10171
neural plate3.91e-0982
presumptive neural plate3.91e-0982
organ system subdivision1.02e-08223
adult organism1.07e-08114
neurectoderm1.62e-0886
caudate nucleus8.31e-082
future caudate nucleus8.31e-082
globus pallidus2.03e-072
pallidum2.03e-072
ecto-epithelium3.09e-07104


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.115.9663
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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

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

This analysis result is provided for C0 - C305 clusters.

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