Personal tools

Coexpression cluster:C4773

From FANTOM5_SSTAR

Revision as of 22:18, 22 January 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4773_gastric_glioblastoma_extraskeletal_adrenal_lung_small_uterus



Phase1 CAGE Peaks

Hg19::chr8:75736712..75736723,+p2@PI15
Hg19::chr8:75736761..75736777,+p1@PI15
Hg19::chr8:75766081..75766085,+p@chr8:75766081..75766085
+


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.14e-32114
neural tube7.43e-2156
neural rod7.43e-2156
future spinal cord7.43e-2156
neural keel7.43e-2156
nervous system7.89e-2189
regional part of nervous system1.51e-1953
regional part of brain1.51e-1953
organ system subdivision2.21e-19223
central nervous system5.85e-1981
neural plate1.49e-1782
presumptive neural plate1.49e-1782
neurectoderm2.92e-1786
brain5.82e-1668
future brain5.82e-1668
structure with developmental contribution from neural crest2.83e-15132
ecto-epithelium3.18e-14104
ectoderm-derived structure1.33e-13171
ectoderm1.33e-13171
presumptive ectoderm1.33e-13171
regional part of forebrain2.65e-1341
forebrain2.65e-1341
anterior neural tube2.65e-1341
future forebrain2.65e-1341
multi-tissue structure1.04e-12342
anatomical cluster1.10e-12373
brain grey matter1.35e-1034
gray matter1.35e-1034
telencephalon3.29e-1034
pre-chordal neural plate4.32e-1061
multi-cellular organism1.97e-09656
organ2.13e-09503
posterior neural tube3.59e-0915
chordal neural plate3.59e-0915
regional part of telencephalon5.06e-0932
cerebral hemisphere6.69e-0932
neural nucleus1.13e-089
nucleus of brain1.13e-089
segmental subdivision of hindbrain6.07e-0812
hindbrain6.07e-0812
presumptive hindbrain6.07e-0812
anatomical system1.42e-07624
anatomical group1.64e-07625
intervertebral cartilage3.25e-075
symphysis3.25e-075
nonsynovial joint3.25e-075
fibrous joint3.25e-075
cartilaginous joint3.25e-075
developing mesenchymal condensation3.25e-075
pre-cartilage condensation3.25e-075
cartilaginous condensation3.25e-075
cartilage element3.25e-075
post-cranial axial skeletal system3.25e-075
vertebral column3.25e-075
intervertebral disk3.25e-075
intervertebral joint3.25e-075
embryo3.36e-07592
segmental subdivision of nervous system3.51e-0713
gastrointestinal system4.91e-0725
embryonic structure7.27e-07564
regional part of metencephalon8.01e-079
metencephalon8.01e-079
future metencephalon8.01e-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)
MA0003.10.0471418
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
MA0038.12.16573
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
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
MA0073.10.0185922
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
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.21.20011
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
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
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.