Personal tools

Coexpression cluster:C3884: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:34, 17 September 2013


Full id: C3884_large_Sebocyte_anaplastic_Keratinocyte_retinoblastoma_papillotubular_carcinoid



Phase1 CAGE Peaks

Hg19::chr1:156783780..156783794,-p7@SH2D2A
Hg19::chr1:156783824..156783836,-p9@SH2D2A
Hg19::chr1:156783894..156783917,-p2@SH2D2A


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.32e-17253
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.77e-11160
endoderm5.77e-11160
presumptive endoderm5.77e-11160
respiratory primordium2.12e-0938
endoderm of foregut2.12e-0938
endo-epithelium5.22e-0982
digestive system6.28e-09145
digestive tract6.28e-09145
primitive gut6.28e-09145
respiratory tract7.55e-0954
larynx1.22e-089
segment of respiratory tract1.09e-0747
subdivision of digestive tract1.31e-07118
respiratory system2.99e-0774
epithelium of mucosa9.19e-078
Disease
Ontology termp-valuen
carcinoma1.06e-21106
cell type cancer3.92e-17143
cancer2.14e-15235
disease of cellular proliferation4.87e-15239
chronic leukemia1.42e-078


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)
MA0003.10.708947
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.12.8588
MA0059.14.12962
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
MA0073.10.668628
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
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
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
MA0141.14.12088
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.70974
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.23.77966
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.12.37721
MA0160.12.02335
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.13.27997
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#90536.336201576962630.003930750035764890.0190110031946489
CTCF#1066435.360256373075030.0064925092527670.027954781243805
CTCFL#140690319.74647435897440.0001298372005551160.00171820418002735
E2F1#186934.907389214879320.008460985347239390.0325484124159392
E2F6#187635.017155731697390.00791769806886330.0322372020043668
EGR1#195834.988179094810140.008056488137383440.0320782144330991
ELF1#199734.258097958807540.01295179875054610.046248389965409
ETS1#211339.728760922202340.001085840092584840.00762636539539124
GABPB1#255337.067683836182170.002832212825417420.0154187591364559
HMGN3#932438.178547723350590.001827766942164210.0108756923241049
MAX#414936.452555509007120.003721913834265510.0186603119839112
MXI1#460139.96157162875930.001011470541259020.00720481324911683
MYC#460935.22228187160940.007020843755740150.0294631695666712
SETDB1#9869340.32002617801051.52461559299059e-050.000358786227842146
SIN3A#2594235.408884726815140.006318961977991520.0276904321746929
SMARCB1#6598318.25271578115740.000164397760679890.00203117682806661
SMARCC1#6599343.66335931963151.20046018043203e-050.000301889864637951
SMC3#9126315.04493284493280.0002935825420371870.00309149698606793
STAT1#6772320.70658749719920.0001125992441046670.00154917039323505
USF1#739136.361499277207960.00388404057290560.0190354440822941
USF2#7392312.99219738506960.0004558979393427810.00421769199105508
ZBTB7A#5134137.35190930787590.002516255860282270.0140269680166544



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3884&oldid=3071001"