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{{Coexpression_clusters
{
|full_id=C4651_argyrophil_colon_Prostate_Intestinal_acute_epidermoid_HES3GFP
 

Latest revision as of 14:17, 17 September 2013


Full id: C4651_argyrophil_colon_Prostate_Intestinal_acute_epidermoid_HES3GFP



Phase1 CAGE Peaks

Hg19::chr7:130126107..130126120,+p4@MEST
Hg19::chr7:130126139..130126152,+p6@MEST
Hg19::chr7:130126165..130126202,+p2@MEST


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

No GOStat results

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 cell2.74e-15253
Uber Anatomy
Ontology termp-valuen
organ system subdivision2.55e-18223
central nervous system3.52e-1481
nervous system1.52e-1189
neural tube1.66e-1156
neural rod1.66e-1156
future spinal cord1.66e-1156
neural keel1.66e-1156
neural plate6.18e-1182
presumptive neural plate6.18e-1182
regional part of nervous system6.93e-1153
regional part of brain6.93e-1153
ecto-epithelium1.35e-10104
pre-chordal neural plate1.88e-1061
brain8.36e-1068
future brain8.36e-1068
regional part of forebrain8.62e-1041
forebrain8.62e-1041
anterior neural tube8.62e-1041
future forebrain8.62e-1041
neurectoderm1.45e-0986
ectoderm-derived structure4.66e-09171
ectoderm4.66e-09171
presumptive ectoderm4.66e-09171
subdivision of digestive tract5.48e-09118
digestive system5.90e-09145
digestive tract5.90e-09145
primitive gut5.90e-09145
telencephalon5.94e-0934
organ part7.41e-09218
cerebral hemisphere8.50e-0932
brain grey matter9.87e-0934
gray matter9.87e-0934
regional part of telencephalon1.20e-0832
endoderm-derived structure1.30e-08160
endoderm1.30e-08160
presumptive endoderm1.30e-08160
adult organism1.92e-08114
cerebral cortex2.71e-0825
pallium2.71e-0825
anatomical cluster3.87e-08373
foregut9.49e-0887
regional part of cerebral cortex2.55e-0722
respiratory primordium3.17e-0738
endoderm of foregut3.17e-0738
respiratory tract7.30e-0754
neocortex8.71e-0720
Disease
Ontology termp-valuen
carcinoma4.27e-24106
cancer5.08e-14235
cell type cancer1.87e-13143
disease of cellular proliferation6.90e-13239


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
MA0048.10.341392
MA0050.11.90116
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0117.13.02823
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.12.53618
MA0143.12.29531
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
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
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
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
CEBPB#105137.971147625824820.001974187055288560.0115780616502292
CTCF#1066435.360256373075030.0064925092527670.0281205645854822
E2F6#187635.017155731697390.00791769806886330.0324217396045487
EGR1#195834.988179094810140.008056488137383440.0322379909800839
ELF1#199734.258097958807540.01295179875054610.046482007824758
GTF2F1#2962312.73966087675770.0004835525047438590.0043588589714262
MAX#414936.452555509007120.003721913834265510.0187367665543649
MYC#460935.22228187160940.007020843755740150.0295975579642264
NANOG#79923329.24477848101273.99627955670032e-050.000740932790027029
NR3C1#2908314.9730233311730.0002978331194675480.0031009264444294
NRF1#4899312.21027944771090.0005492172401020010.00473382019798736
RAD21#5885310.35503389545630.0009004912073565420.00668370415785018
SMC3#9126315.04493284493280.0002935825420371870.0031071612391388
TAF7#6879311.43306940492390.0006690181981945830.0054557344890485
TCF12#6938310.63446490218640.0008313523990202070.00631918582250883
TFAP2A#7020316.5186343730450.0002218033880766340.0024943387581927
TFAP2C#7022310.80922860986020.0007916746575753130.0061882875205829
YY1#752834.911170749853860.008441455341808260.0331136250917635
ZEB1#6935211.25895467836260.01010222676646330.0378268486039961



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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