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Latest revision as of 03:15, 17 September 2013


Full id: C2934_heart_left_Mast_Whole_skeletal_tongue_neuroblastoma



Phase1 CAGE Peaks

  Short description
Hg19::chr9:100263912..100263988,+ p1@TMOD1
Hg19::chr9:100263992..100264003,+ p2@TMOD1
Hg19::chr9:100264007..100264012,+ p5@TMOD1
Hg19::chr9:100264015..100264024,+ p3@TMOD1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism1.93e-76114
neural tube3.27e-2956
neural rod3.27e-2956
future spinal cord3.27e-2956
neural keel3.27e-2956
central nervous system1.38e-2781
nervous system5.45e-2789
regional part of nervous system9.57e-2753
regional part of brain9.57e-2753
brain2.03e-2468
future brain2.03e-2468
organ system subdivision1.96e-22223
regional part of forebrain4.39e-2241
forebrain4.39e-2241
anterior neural tube4.39e-2241
future forebrain4.39e-2241
neural plate1.31e-1982
presumptive neural plate1.31e-1982
telencephalon2.02e-1834
brain grey matter2.19e-1834
gray matter2.19e-1834
neurectoderm8.36e-1886
regional part of cerebral cortex9.60e-1822
cerebral hemisphere3.30e-1732
regional part of telencephalon4.99e-1732
neocortex2.31e-1620
cerebral cortex1.14e-1425
pallium1.14e-1425
structure with developmental contribution from neural crest3.36e-13132
ecto-epithelium7.39e-13104
pre-chordal neural plate2.01e-1261
ectoderm-derived structure8.78e-11171
ectoderm8.78e-11171
presumptive ectoderm8.78e-11171
anatomical cluster9.83e-11373
posterior neural tube2.92e-0815
chordal neural plate2.92e-0815
anatomical conduit1.67e-07240
multi-tissue structure2.28e-07342
tube3.91e-07192
developing anatomical structure8.40e-07581
organ9.41e-07503
germ layer9.42e-07560
germ layer / neural crest9.42e-07560
embryonic tissue9.42e-07560
presumptive structure9.42e-07560
germ layer / neural crest derived structure9.42e-07560
epiblast (generic)9.42e-07560


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.111.7073
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
MA0017.10.577281
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
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.53734
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.11.90157
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
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
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.12.92476
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.24.95563
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.211.2591
MA0102.21.75932
MA0258.11.07498
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90546.336201576962630.0006203100587215640.00513959240165184
CTCF#1066445.360256373075030.001211145381643620.00820569656266483
E2F1#186944.907389214879320.001724022357361790.0106870353146075
ELF1#199744.258097958807540.003041525565781240.0161343909266877
HDAC2#3066413.41562023662633.0859005065161e-050.000629100845207954
PAX5#507946.669565531177830.0005052774169483260.00445134273712916
RAD21#5885410.35503389545638.6948481184721e-050.0013017219648009
SPI1#668848.204323508522730.000220661881527680.00249980542844879
TCF7L2#6934410.77017656313737.42969445082454e-050.00115882595392722



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.