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{{Coexpression_clusters
{
|full_id=C2599_pineal_pituitary_cerebellum_spinal_thalamus_parietal_hippocampus
|

Latest revision as of 12:09, 17 September 2013


Full id: C2599_pineal_pituitary_cerebellum_spinal_thalamus_parietal_hippocampus



Phase1 CAGE Peaks

Hg19::chr1:78470530..78470551,+p7@DNAJB4
Hg19::chr4:186317034..186317083,-p1@LRP2BP
Hg19::chr4:331318..331341,-p@chr4:331318..331341
-
Hg19::chr7:95174494..95174520,+p@chr7:95174494..95174520
+


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:0009408response to heat0.0137736177222909
GO:0009266response to temperature stimulus0.0153592627850831
GO:0006986response to unfolded protein0.0156171759566238
GO:0051789response to protein stimulus0.0156171759566238
GO:0031072heat shock protein binding0.0215856666907313
GO:0009628response to abiotic stimulus0.0290713032697566
GO:0051082unfolded protein binding0.030188354377766
GO:0009607response to biotic stimulus0.0381192540324227
GO:0006457protein folding0.0404160150686843



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 organism1.44e-45114
neural tube4.50e-2656
neural rod4.50e-2656
future spinal cord4.50e-2656
neural keel4.50e-2656
regional part of nervous system2.98e-2453
regional part of brain2.98e-2453
regional part of forebrain2.42e-2241
forebrain2.42e-2241
anterior neural tube2.42e-2241
future forebrain2.42e-2241
brain1.45e-2068
future brain1.45e-2068
central nervous system1.21e-1981
neural plate8.55e-1982
presumptive neural plate8.55e-1982
brain grey matter1.02e-1734
gray matter1.02e-1734
telencephalon1.02e-1734
nervous system1.10e-1789
neurectoderm2.25e-1786
regional part of telencephalon1.86e-1632
cerebral hemisphere2.13e-1632
pre-chordal neural plate9.10e-1561
regional part of cerebral cortex1.44e-1322
neocortex2.73e-1220
structure with developmental contribution from neural crest2.87e-12132
cerebral cortex4.12e-1225
pallium4.12e-1225
ecto-epithelium8.41e-12104
ectoderm-derived structure1.50e-07171
ectoderm1.50e-07171
presumptive ectoderm1.50e-07171
neural nucleus2.97e-079
nucleus of brain2.97e-079
basal ganglion3.16e-079
nuclear complex of neuraxis3.16e-079
aggregate regional part of brain3.16e-079
collection of basal ganglia3.16e-079
cerebral subcortex3.16e-079
organ system subdivision3.70e-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)
MA0003.10.443649
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.12.05499
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
BCLAF1#9774210.82632380506090.01202203816432580.0436583206594117
GTF2B#2959215.97191496716210.005636585723537220.0254751331305394
JUN#372539.384621894252250.001918994502030470.0112866963337028
JUND#372735.245997956403270.01043432751748420.0386999087893225
KAT2A#26481154.02250.006476819949311040.0281260955794634
POLR3A#11128184.78302752293580.01174284177711620.0428650048009589
RFX5#599339.035933120396320.002144561191324070.0123853033765038



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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