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{{Coexpression_clusters
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|full_id=C3300_acute_lymphoma_chronic_giant_Fibroblast_hereditary_diffuse
|gostat_on_coexpression_clusters=GO:0042254!ribosome biogenesis and assembly!0.000846401070932352!51154;5036$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.00208896775368931!51154;5036$GO:0004239!methionyl aminopeptidase activity!0.0188359938245719!5036$GO:0050897!cobalt ion binding!0.0211886214040835!5036$GO:0006996!organelle organization and biogenesis!0.0322637551551224!51154;5036$GO:0006364!rRNA processing!0.0488047959039513!5036$GO:0016072!rRNA metabolic process!0.0488047959039513!5036$GO:0004177!aminopeptidase activity!0.0488047959039513!5036
|id=C3300
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3300_acute_lymphoma_chronic_giant_Fibroblast_hereditary_diffuse



Phase1 CAGE Peaks

Hg19::chr12:56498312..56498413,+p1@PA2G4
Hg19::chr1:19578280..19578334,+p1@MRTO4
Hg19::chr5:175815565..175815615,-p1@NOP16


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:0042254ribosome biogenesis and assembly0.000846401070932352
GO:0022613ribonucleoprotein complex biogenesis and assembly0.00208896775368931
GO:0004239methionyl aminopeptidase activity0.0188359938245719
GO:0050897cobalt ion binding0.0211886214040835
GO:0006996organelle organization and biogenesis0.0322637551551224
GO:0006364rRNA processing0.0488047959039513
GO:0016072rRNA metabolic process0.0488047959039513
GO:0004177aminopeptidase activity0.0488047959039513



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 cell2.87e-27253
animal cell2.76e-25679
eukaryotic cell2.76e-25679
embryonic cell5.36e-19250
native cell1.15e-13722
squamous epithelial cell2.26e-1063
mesodermal cell3.49e-08121
somatic cell8.65e-07588
Uber Anatomy
Ontology termp-valuen
trunk2.75e-08199
unilaminar epithelium4.15e-08148
organism subdivision1.18e-07264
segment of respiratory tract1.50e-0747
respiratory primordium1.98e-0738
endoderm of foregut1.98e-0738
larynx2.65e-079
Disease
Ontology termp-valuen
disease of cellular proliferation1.45e-32239
cancer3.18e-32235
hematologic cancer1.19e-1851
immune system cancer1.19e-1851
organ system cancer1.23e-16137
leukemia2.54e-1539
cell type cancer1.12e-14143
carcinoma1.94e-13106
myeloid leukemia4.69e-1331


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)
MA0003.11.0927
MA0004.10.826076
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
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
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
MA0088.15.67475
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
MA0105.11.5295
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
MA0141.12.84752
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
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
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
BCLAF1#9774214.43509840674790.006201147435546130.0273751643004904
CHD2#1106310.34402283411690.0009033701102746880.00659078385937675
E2F1#186934.907389214879320.008460985347239390.0324111226775357
E2F6#187635.017155731697390.00791769806886330.0320958107675056
ELF1#199734.258097958807540.01295179875054610.0460656896100083
ESRRA#21011161.2801047120420.006187620080219560.0273478143697863
ETS1#211339.728760922202340.001085840092584840.00760692604168686
GABPB1#255337.067683836182170.002832212825417420.0153738812512355
MAX#414936.452555509007120.003721913834265510.0186031566851809
MXI1#460139.96157162875930.001011470541259020.00718961218665698
MYC#460935.22228187160940.007020843755740150.0293546539495475
NFKB1#479035.488063424193840.006049381815655430.0268916058332016
NR2C2#7182221.74307393682720.002762207975496010.0151362736110409
PPARGC1A#108911116.6837121212120.008545763211786680.0325638851457892
SIN3A#2594235.408884726815140.006318961977991520.0275758845904837
SIX5#147912211.3911435703060.009873820081429030.0370606251746403
SMARCB1#6598212.16847718743830.008675002221921740.0329733434165042
SP1#666735.69838137814090.005403962701712170.0245715730159832
SPI1#668838.204323508522730.001810593189410520.0108914031856264
STAT1#6772213.80439166479950.006770931708444080.0287459079958614
TRIM28#10155212.39368336350830.008368344129438470.0328923071218405
USF1#739136.361499277207960.00388404057290560.0189713456829898
YY1#752834.911170749853860.008441455341808260.032833680475331
ZBTB33#10009221.10981668665410.002928597060603240.0156298098222874
ZBTB7A#5134137.35190930787590.002516255860282270.0139769836077023
ZEB1#6935211.25895467836260.01010222676646330.0378051620059717
ZNF143#7702313.50087655222790.0004062804962997170.00388105083262106
ZNF263#1012738.221841637010680.001799043925565870.0109054703431525



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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