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Coexpression cluster:C2400: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.45381,MA0004.1;1.69588,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;1.35734,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.866596,MA0074.1;0.819248,MA0076.1;2.5647,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;1.32557,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;4.47134,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.569905,MA0146.1;0.221129,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;3.45291,MA0035.2;0.778873,MA0039.2;1.5472,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;1.02191,MA0156.1;1.37856,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.640035,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.476674,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:38, 22 January 2013


Full id: C2400_Alveolar_embryonic_Mesenchymal_Renal_Smooth_acute_granulocyte



Phase1 CAGE Peaks

Hg19::chr17:33469299..33469328,-p1@NLE1
Hg19::chr19:13044513..13044543,-p1@FARSA
Hg19::chr19:48949218..48949267,+p1@GRWD1
Hg19::chr19:56166360..56166452,+p1@U2AF2


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:0001826inner cell mass cell differentiation0.00977232251375934
GO:0001825blastocyst formation0.00977232251375934
GO:0006432phenylalanyl-tRNA aminoacylation0.0146558949108512
GO:0004826phenylalanine-tRNA ligase activity0.0146558949108512
GO:0001824blastocyst development0.0273480076998137



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
animal cell3.42e-28679
eukaryotic cell3.42e-28679
epithelial cell5.93e-23253
embryonic cell2.84e-21250
native cell4.20e-18722
mesodermal cell1.63e-12121
somatic cell4.73e-10588
non-terminally differentiated cell3.66e-09106
contractile cell2.44e-0859
squamous epithelial cell3.25e-0863
electrically responsive cell1.23e-0761
electrically active cell1.23e-0761
muscle cell4.99e-0755
muscle precursor cell6.52e-0758
myoblast6.52e-0758
multi-potent skeletal muscle stem cell6.52e-0758
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium4.00e-11148
epithelial vesicle1.90e-1078
epithelial tube2.69e-10117
trunk3.12e-10199
vessel1.88e-0868
multilaminar epithelium2.19e-0883
epithelial tube open at both ends2.40e-0859
blood vessel2.40e-0859
blood vasculature2.40e-0859
vascular cord2.40e-0859
mesenchyme2.96e-08160
entire embryonic mesenchyme2.96e-08160
vasculature3.71e-0878
vascular system3.71e-0878
somite5.72e-0871
presomitic mesoderm5.72e-0871
presumptive segmental plate5.72e-0871
dermomyotome5.72e-0871
trunk paraxial mesoderm5.72e-0871
splanchnic layer of lateral plate mesoderm6.28e-0883
organism subdivision6.30e-08264
artery9.11e-0842
arterial blood vessel9.11e-0842
arterial system9.11e-0842
trunk mesenchyme1.04e-07122
paraxial mesoderm1.36e-0772
presumptive paraxial mesoderm1.36e-0772
dense mesenchyme tissue3.09e-0773
segment of respiratory tract4.48e-0747
respiratory primordium7.76e-0738
endoderm of foregut7.76e-0738
Disease
Ontology termp-valuen
cancer1.84e-20235
disease of cellular proliferation6.65e-20239
hematologic cancer4.71e-1551
immune system cancer4.71e-1551
leukemia2.18e-1339
myeloid leukemia3.25e-1231
organ system cancer1.78e-11137
cell type cancer5.30e-09143
carcinoma5.82e-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)
MA0003.11.45381
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.12.5647
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.14.47134
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.221129
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.23.45291
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#90546.336201576962630.0006203100587215640.00511888133871851
ELF1#199744.258097958807540.003041525565781240.0160804843861814
ETS1#211337.296570691651750.00400857377511390.0192024326437538
GABPB1#255335.300762877136630.01012678824234270.0378550283561341
HEY1#2346244.040111043105710.00375304636917980.0185897277567356
HMGN3#932436.133910792512940.006640696683324720.028291903439249
MAX#414934.839416631755340.01315737137836840.0466142918479397
MXI1#460137.471178721569470.003741314738550960.0186323575403902
POU2F2#545236.829593043306890.004860473775203740.0227572411283288
POU5F1#5460183.85980036297640.01187154239091560.0432395904221536
TAF1#687243.343046285745290.008005664898701650.0321949802216212
TBP#690843.706770687096390.005296377814784350.0243978653227886
USF1#739134.771124457905970.01370465887188020.048294391062533
USF2#739239.74414803880220.001718341848410070.01071798281809
XRCC4#751811074.575581395350.0009302828080034460.00674379164191518
YY1#752844.911170749853860.00171871838055440.0106769705535761



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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