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Coexpression cluster:C3999: Difference between revisions

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{{Coexpression_clusters
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2.30945,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.05956,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;6.30148,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3999_anaplastic_Fibroblast_putamen_caudate_eye_frontal_testis
|id=C3999
}}

Latest revision as of 12:37, 17 September 2013


Full id: C3999_anaplastic_Fibroblast_putamen_caudate_eye_frontal_testis



Phase1 CAGE Peaks

Hg19::chr1:85155895..85155909,-p5@SSX2IP
Hg19::chr1:85155912..85155935,-p3@SSX2IP
Hg19::chr1:85155939..85155984,-p2@SSX2IP


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
regional part of forebrain1.70e-1941
forebrain1.70e-1941
anterior neural tube1.70e-1941
future forebrain1.70e-1941
cerebral hemisphere1.08e-1832
central nervous system3.15e-1881
nervous system1.51e-1789
telencephalon1.81e-1734
regional part of telencephalon4.24e-1732
brain1.10e-1668
future brain1.10e-1668
brain grey matter1.61e-1534
gray matter1.61e-1534
cerebral cortex2.44e-1525
pallium2.44e-1525
regional part of nervous system2.89e-1553
regional part of brain2.89e-1553
organ system subdivision3.82e-15223
regional part of cerebral cortex8.34e-1422
neural tube8.93e-1456
neural rod8.93e-1456
future spinal cord8.93e-1456
neural keel8.93e-1456
pre-chordal neural plate2.58e-1361
neocortex8.11e-1320
ectoderm-derived structure6.43e-11171
ectoderm6.43e-11171
presumptive ectoderm6.43e-11171
neural plate1.26e-1082
presumptive neural plate1.26e-1082
neurectoderm4.38e-1086
ecto-epithelium1.35e-09104
structure with developmental contribution from neural crest3.08e-07132
adult organism4.40e-07114
Disease
Ontology termp-valuen
disease of cellular proliferation9.23e-12239
cancer1.09e-10235
cell type cancer5.18e-08143
carcinoma8.99e-08106


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)
MA0003.14.57391
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0073.12.78116
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
MA0100.13.60951
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
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
MA0039.22.15877
MA0138.23.88672
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
MA0154.12.30945
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.30148
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

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

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0190259815074037
CHD2#1106310.34402283411690.0009033701102746880.00660878894276956
E2F1#186934.907389214879320.008460985347239390.0325760100523606
E2F6#187635.017155731697390.00791769806886330.0322673925396657
EGR1#195834.988179094810140.008056488137383440.0321039171498412
ELF1#199734.258097958807540.01295179875054610.046286371123333
FOS#235338.99795530889440.001372499272417130.00898360814188848
GATA1#2623313.56030814380040.0004009615963782630.00388280279686133
IRF1#365937.63716375356390.002244692747297240.0128224835002449
NFYA#4800212.28372046655370.008516011403724430.0324813276967926
NFYB#4801316.75979325353650.0002123649923296180.00246107272901831
SP1#666735.69838137814090.005403962701712170.0246822557773164
SRF#6722313.79717826216780.0003806615025800190.00375374437427576
TFAP2A#7020316.5186343730450.0002218033880766340.00248417416057218
TFAP2C#7022310.80922860986020.0007916746575753130.00616337752981797
ZBTB7A#5134137.35190930787590.002516255860282270.01403820757436



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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