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Coexpression cluster:C4496: Difference between revisions

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{{Coexpression_clusters
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constituent of nuclear pore!0.00989049805722359!9631$GO:0065002!intracellular protein transport across a membrane!0.014257730965608!9631$GO:0051028!mRNA transport!0.014257730965608!9631$GO:0005643!nuclear pore!0.014257730965608!9631$GO:0050658!RNA transport!0.014257730965608!9631$GO:0051236!establishment of RNA localization!0.014257730965608!9631$GO:0050657!nucleic acid transport!0.014257730965608!9631$GO:0006403!RNA localization!0.014257730965608!9631$GO:0046930!pore complex!0.014257730965608!9631$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.014257730965608!9631$GO:0044453!nuclear membrane part!0.014257730965608!9631$GO:0031965!nuclear membrane!0.0157440581319069!9631$GO:0006913!nucleocytoplasmic transport!0.0157440581319069!9631$GO:0051169!nuclear transport!0.0157440581319069!9631$GO:0005635!nuclear envelope!0.0182738726009655!9631$GO:0006886!intracellular protein transport!0.0467149417167079!9631$GO:0031967!organelle 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|full_id=C4496_oral_chronic_small_Hep2_cervical_choriocarcinoma_synovial
|id=C4496
}}

Latest revision as of 12:46, 17 September 2013


Full id: C4496_oral_chronic_small_Hep2_cervical_choriocarcinoma_synovial



Phase1 CAGE Peaks

Hg19::chr5:34915771..34915791,+p3@BRIX1
Hg19::chr5:34915805..34915847,+p1@BRIX1
Hg19::chr5:37371163..37371231,-p1@NUP155


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:0017056structural constituent of nuclear pore0.00989049805722359
GO:0065002intracellular protein transport across a membrane0.014257730965608
GO:0051028mRNA transport0.014257730965608
GO:0005643nuclear pore0.014257730965608
GO:0050658RNA transport0.014257730965608
GO:0051236establishment of RNA localization0.014257730965608
GO:0050657nucleic acid transport0.014257730965608
GO:0006403RNA localization0.014257730965608
GO:0046930pore complex0.014257730965608
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.014257730965608
GO:0044453nuclear membrane part0.014257730965608
GO:0031965nuclear membrane0.0157440581319069
GO:0006913nucleocytoplasmic transport0.0157440581319069
GO:0051169nuclear transport0.0157440581319069
GO:0005635nuclear envelope0.0182738726009655
GO:0006886intracellular protein transport0.0467149417167079
GO:0031967organelle envelope0.0489815141881549
GO:0031975envelope0.0489815141881549



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 cell1.06e-08253
nucleate cell3.10e-0855
lymphocyte1.32e-0753
common lymphoid progenitor1.32e-0753
lymphoid lineage restricted progenitor cell2.71e-0752
Uber Anatomy
Ontology termp-valuen
larynx1.24e-079
Disease
Ontology termp-valuen
cancer5.64e-66235
disease of cellular proliferation2.49e-64239
cell type cancer3.23e-44143
carcinoma4.99e-37106
organ system cancer1.87e-25137
hematologic cancer1.35e-1551
immune system cancer1.35e-1551
leukemia4.78e-1339
myeloid leukemia1.65e-1031
disease of anatomical entity6.01e-0739
germ cell and embryonal cancer6.65e-0722
germ cell cancer6.65e-0722
respiratory system cancer8.36e-0716


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
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
MA0057.10.333427
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
MA0073.10.990225
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
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
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
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
MA0062.21.9924
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
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
BCLAF1#9774214.43509840674790.006201147435546130.0273971672668472
CCNT2#90536.336201576962630.003930750035764890.0190870189225055
E2F1#186934.907389214879320.008460985347239390.0327147032201819
E2F4#1874312.66806031528440.0004917987006298980.00438549901768152
E2F6#187635.017155731697390.00791769806886330.0323899909367025
EGR1#195834.988179094810140.008056488137383440.0322083740843741
ELF1#199734.258097958807540.01295179875054610.0464437050543617
ELK4#2005316.2356816584680.0002336043955745990.0025622148151035
ETS1#211339.728760922202340.001085840092584840.00764435816848451
GABPB1#255337.067683836182170.002832212825417420.015468751975409
GTF2F1#2962312.73966087675770.0004835525047438590.00435472450141795
HMGN3#932438.178547723350590.001827766942164210.0109061390431748
IRF1#365937.63716375356390.002244692747297240.0128604677072235
JUNB#3726220.40708843988080.003131462199438740.0164551839319337
KAT2A#26481205.3633333333330.004861545220737780.022755116806733
MAX#414936.452555509007120.003721913834265510.0187241309699834
MXI1#460139.96157162875930.001011470541259020.00722402871220345
MYC#460935.22228187160940.007020843755740150.0295677205131556
NFKB1#479035.488063424193840.006049381815655430.027058605826598
NR3C1#290829.982015554115360.01278474365547170.0460708661456701
PAX5#507936.669565531177830.003370290999677260.0173530773868711
REST#597839.650028716128020.001112636247114590.00770421116570978
RFX5#5993312.04791082719510.0005717246050312580.00486121843400306
SIN3A#2594235.408884726815140.006318961977991520.0277942246470458
SIX5#147912317.0867153554590.0002004060546325010.00240245729336132
SMC3#9126210.02995522995520.0126656379767470.0457806660432436
SP1#666735.69838137814090.005403962701712170.0247623929713986
SP2#6668217.43568699589640.004273568481769740.0203282573632515
SPI1#668838.204323508522730.001810593189410520.010934228177914
SRF#6722313.79717826216780.0003806615025800190.00376084634073925
TCF12#6938310.63446490218640.0008313523990202070.00631321262279294
TCF7L2#6934310.77017656313730.0008003181298398380.00616495243858555
TFAP2A#7020211.01242291536330.01054990655215560.0390329350432402
TFAP2C#7022310.80922860986020.0007916746575753130.00618181006074827
THAP1#55145331.36914460285133.23800758564397e-050.000648588941766534
TRIM28#10155318.59052504526250.0001555969297255280.00197741393813633
YY1#752834.911170749853860.008441455341808260.0330875269072289
ZNF263#1012738.221841637010680.001799043925565870.0109922394279632



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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