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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 11:46, 17 September 2013


Full id: C1518_non_optic_corpus_thalamus_globus_substantia_medulla



Phase1 CAGE Peaks

Hg19::chr4:144257353..144257371,+p@chr4:144257353..144257371
+
Hg19::chr4:144257585..144257614,+p4@GAB1
Hg19::chr4:144257672..144257687,+p2@GAB1
Hg19::chr4:144257996..144258009,+p6@GAB1
Hg19::chr4:144258021..144258052,+p1@GAB1
Hg19::chr4:144258062..144258073,+p9@GAB1


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

No GOStat results

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 organism1.48e-47114
neural tube1.35e-2456
neural rod1.35e-2456
future spinal cord1.35e-2456
neural keel1.35e-2456
central nervous system3.28e-2381
regional part of nervous system9.38e-2353
regional part of brain9.38e-2353
regional part of forebrain2.79e-2141
forebrain2.79e-2141
anterior neural tube2.79e-2141
future forebrain2.79e-2141
nervous system3.77e-2089
brain8.09e-2068
future brain8.09e-2068
telencephalon3.13e-1834
brain grey matter3.17e-1834
gray matter3.17e-1834
regional part of telencephalon5.64e-1732
cerebral hemisphere6.96e-1732
neural plate1.85e-1582
presumptive neural plate1.85e-1582
organ system subdivision2.89e-14223
neurectoderm3.02e-1486
cerebral cortex6.17e-1325
pallium6.17e-1325
ectoderm-derived structure2.00e-12171
ectoderm2.00e-12171
presumptive ectoderm2.00e-12171
ecto-epithelium7.09e-12104
regional part of cerebral cortex7.39e-1222
pre-chordal neural plate2.25e-1161
neocortex8.17e-1120
organ8.39e-11503
anatomical conduit7.32e-10240
multi-cellular organism1.58e-09656
structure with developmental contribution from neural crest1.17e-08132
anatomical group2.63e-08625
anatomical system3.14e-08624
anatomical cluster8.61e-08373
tube4.00e-07192
embryonic structure5.96e-07564
neural nucleus7.77e-079
nucleus of brain7.77e-079


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)
MA0003.15.21839
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.11.935
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.22849
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.16.01556
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.12.32368
MA0115.12.85672
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.13.45912
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.11.44958
MA0147.10.327615
MA0148.10.584698
MA0149.12.52795
MA0062.20.23336
MA0035.20.621793
MA0039.21.47843
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.12.40092
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.49373
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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
E2F1#186954.089491012399440.001749817597761990.010760080080821
GTF2B#2959315.97191496716210.0005711653715892990.00486795660546881
HEY1#2346264.040111043105710.0002298968555807510.00253432527971269
NR2C2#7182527.17884242103411.5816706961502e-078.84778285137819e-06
POLR2A#543062.147453176558070.01019570676818780.0380636074767745
SMARCB1#659839.126357890578710.002900247150367020.0156788090551882
SPI1#668856.836936257102270.0001449641773974030.00188612354842499
TAF1#687263.343046285745290.0007162474284635620.00573607585164527
TCF12#693835.317232451093210.013367345733860.0472492036788372



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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