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{{Coexpression_clusters
{
|full_id=C3036_Mast_CD14_diffuse_Reticulocytes_chronic_acute_teratocarcinoma
|

Latest revision as of 12:17, 17 September 2013


Full id: C3036_Mast_CD14_diffuse_Reticulocytes_chronic_acute_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr10:70091812..70091830,+p1@HNRNPH3
Hg19::chr10:70091847..70091858,+p2@HNRNPH3
Hg19::chr7:26240357..26240377,-p1@HNRNPA2B1


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:0043047single-stranded telomeric DNA binding0.00565171317555634
GO:0042162telomeric DNA binding0.00847756976333451
GO:0030530heterogeneous nuclear ribonucleoprotein complex0.00847756976333451
GO:0003697single-stranded DNA binding0.0118172184579814
GO:0000375RNA splicing, via transesterification reactions0.0118172184579814
GO:0000398nuclear mRNA splicing, via spliceosome0.0118172184579814
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0118172184579814
GO:0050658RNA transport0.0118172184579814
GO:0051236establishment of RNA localization0.0118172184579814
GO:0050657nucleic acid transport0.0118172184579814
GO:0006403RNA localization0.0118172184579814
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0122453785470387
GO:0005681spliceosome0.0151074640654294
GO:0043566structure-specific DNA binding0.0160468284805975
GO:0008380RNA splicing0.0211939244083363
GO:0006397mRNA processing0.0241080890144825
GO:0016071mRNA metabolic process0.0284247927358863
GO:0006396RNA processing0.041210408571765



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>

Disease
Ontology termp-valuen
cancer4.39e-23235
disease of cellular proliferation2.05e-21239
hematologic cancer1.12e-1251
immune system cancer1.12e-1251
organ system cancer1.73e-11137
leukemia1.88e-1139
cell type cancer4.39e-11143
myeloid leukemia5.45e-0931
carcinoma1.22e-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)
MA0003.10.708947
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
MA0038.10.94098
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
MA0055.11.67416
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
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.12.19699
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
MA0002.20.476938
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
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
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
BCL3#602334.54710280373832.42397750207122e-050.000526206165742707
BCLAF1#9774321.65264761012189.8473954032885e-050.00138811192944263
BRCA1#672213.45615376214920.007119807716084560.0296072306613639
CCNT2#90536.336201576962630.003930750035764890.0189076825251128
E2F1#186934.907389214879320.008460985347239390.0323435031177605
E2F4#1874312.66806031528440.0004917987006298980.00435205596467429
E2F6#187635.017155731697390.00791769806886330.0320286803243479
EGR1#195834.988179094810140.008056488137383440.0318946046237894
ELF1#199734.258097958807540.01295179875054610.0459873838889061
EP300#203336.77394172622320.003216880500103790.0166799614015659
ETS1#211339.728760922202340.001085840092584840.00759622569692998
FOSL2#2355211.28680040304110.0100534586973120.0376563918118052
GTF2B#2959331.94382993432423.06634405746243e-050.00062572471085838
GTF2F1#2962312.73966087675770.0004835525047438590.00432674263561891
HNF4G#3174219.16894835096450.003543986611284220.0179657517569125
IRF1#365937.63716375356390.002244692747297240.0127582838549647
JUND#372736.994663941871030.002921845042734990.0156121239342167
MAX#414936.452555509007120.003721913834265510.0185640650908284
MEF2A#4205212.4954872730960.008235029478029740.0324685055553606
MEF2C#4208227.54090299508270.001729119938369690.0106447130706391
MYC#460935.22228187160940.007020843755740150.0293100651958966
NANOG#79923219.49651898734180.003427255648501020.0174417285193353
NFKB1#479035.488063424193840.006049381815655430.0268470397928542
NR3C1#2908314.9730233311730.0002978331194675480.00307821802712234
NRF1#4899312.21027944771090.0005492172401020010.00469238378100564
PAX5#507936.669565531177830.003370290999677260.0172214796083612
PBX3#5090214.60967512449610.006056122473217890.0268051947355655
POU2F2#545239.106124057742520.001324165192682130.008792884572643
RDBP#79363153.6384039900252.75057764221434e-071.39653659881003e-05
REST#597839.650028716128020.001112636247114590.00765195686898463
RXRA#6256213.38307809275550.007196434429465730.029815471889042
SIN3A#2594235.408884726815140.006318961977991520.0275321681276369
SP1#666735.69838137814090.005403962701712170.0245363212157255
STAT2#6773243.50918079096040.0006968990898868230.00560605746350535
TAF7#6879311.43306940492390.0006690181981945830.00540383539066079
TCF12#6938310.63446490218640.0008313523990202070.00627579423211213
TRIM28#10155212.39368336350830.008368344129438470.0328898315031959
USF1#739136.361499277207960.00388404057290560.0189447652434937
WRNIP1#56897273.21330956625070.000247093641135960.00268451188875465
YY1#752834.911170749853860.008441455341808260.0327799648426515
ZBTB33#10009331.66472502998123.14815888737575e-050.000632898105945402
ZEB1#6935316.88843201754390.0002075486917327580.00241840653976096



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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