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Coexpression cluster:C2971: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.05336,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;2.72668,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;2.13518,MA0061.1;2.01615,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0834661,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;2.4174,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.707589,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.711948,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;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;2.26143,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:02, 22 January 2013


Full id: C2971_Mast_rhabdomyosarcoma_osteosarcoma_hepatoblastoma_malignant_acute_hepatocellular



Phase1 CAGE Peaks

Hg19::chr10:103912137..103912159,+p1@NOLC1
Hg19::chr2:232329186..232329215,-p1@NCL
Hg19::chrX:153991175..153991226,+p2@DKC1


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:0005730nucleolus1.09134518659741e-05
GO:0031981nuclear lumen0.000340050982291448
GO:0006364rRNA processing0.000340050982291448
GO:0016072rRNA metabolic process0.000340050982291448
GO:0031974membrane-enclosed lumen0.000376365868350794
GO:0043233organelle lumen0.000376365868350794
GO:0042254ribosome biogenesis and assembly0.000419565009273174
GO:0044428nuclear part0.000419565009273174
GO:0022613ribonucleoprotein complex biogenesis and assembly0.00168049642567982
GO:0003720telomerase activity0.00342604853543545
GO:0005697telomerase holoenzyme complex0.00389312236399137
GO:0043232intracellular non-membrane-bound organelle0.00473375331587104
GO:0043228non-membrane-bound organelle0.00473375331587104
GO:0006396RNA processing0.00490394377798006
GO:0031119tRNA pseudouridine synthesis0.00570907239064743
GO:0007004telomere maintenance via telomerase0.00909695917889302
GO:0001522pseudouridine synthesis0.00916701121882851
GO:0044446intracellular organelle part0.00916701121882851
GO:0044422organelle part0.00916701121882851
GO:0006400tRNA modification0.00941664197669587
GO:0003723RNA binding0.0107915548678622
GO:0032200telomere organization and biogenesis0.0107915548678622
GO:0000723telomere maintenance0.0107915548678622
GO:0016439tRNA-pseudouridine synthase activity0.011766990608002
GO:0009982pseudouridine synthase activity0.0126640690375726
GO:0009451RNA modification0.014806363407018
GO:0003964RNA-directed DNA polymerase activity0.0158398668910636
GO:0006278RNA-dependent DNA replication0.0181666133021973
GO:0005938cell cortex0.0181666133021973
GO:0005634nucleus0.0181666133021973
GO:0006996organelle organization and biogenesis0.0181666133021973
GO:0016866intramolecular transferase activity0.0181666133021973
GO:0008022protein C-terminus binding0.0191670845322766
GO:0008033tRNA processing0.0231162234769279
GO:0001525angiogenesis0.0314525679379851
GO:0048514blood vessel morphogenesis0.0348272231545753
GO:0048646anatomical structure formation0.0352628088452944
GO:0001568blood vessel development0.0362830862796039
GO:0001944vasculature development0.0362830862796039
GO:0043231intracellular membrane-bound organelle0.0414910712264059
GO:0043227membrane-bound organelle0.0414910712264059
GO:0006399tRNA metabolic process0.0441775786977901
GO:0016779nucleotidyltransferase activity0.0453127893723849
GO:0007067mitosis0.0462030726886151
GO:0000087M phase of mitotic cell cycle0.0463022736324971



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell4.34e-14253
Disease
Ontology termp-valuen
cancer1.13e-61235
disease of cellular proliferation7.55e-61239
cell type cancer1.21e-33143
organ system cancer3.40e-28137
carcinoma1.63e-27106
hematologic cancer6.35e-2251
immune system cancer6.35e-2251
leukemia1.02e-1839
myeloid leukemia3.87e-1531
squamous cell carcinoma7.64e-0714
germ cell and embryonal cancer8.40e-0722
germ cell cancer8.40e-0722


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)
MA0003.12.05336
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
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
MA0131.12.4174
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
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
ATF3#467214.97544968400580.005768294540793880.0259401874589206
BCLAF1#9774214.43509840674790.006201147435546130.027369379918903
E2F1#186934.907389214879320.008460985347239390.0323281206073145
E2F4#1874312.66806031528440.0004917987006298980.00435021296646786
E2F6#187635.017155731697390.00791769806886330.032016279565356
ELF1#199734.258097958807540.01295179875054610.045970192343527
FOSL2#2355211.28680040304110.0100534586973120.0376523407046032
IRF1#365937.63716375356390.002244692747297240.0127534254071906
MAX#414936.452555509007120.003721913834265510.0185614057366467
MYC#460935.22228187160940.007020843755740150.0292995245347137
NFKB1#479035.488063424193840.006049381815655430.0268401965863137
SIN3A#2594235.408884726815140.006318961977991520.0275241302089276
SP1#666735.69838137814090.005403962701712170.0245288565606553
YY1#752834.911170749853860.008441455341808260.0327702172413156



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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