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{{Coexpression_clusters
{
|full_id=C4856_pituitary_cerebellum_pineal_Fibroblast_liposarcoma_acute_colon
 

Latest revision as of 14:21, 17 September 2013


Full id: C4856_pituitary_cerebellum_pineal_Fibroblast_liposarcoma_acute_colon



Phase1 CAGE Peaks

Hg19::chrX:1510670..1510699,+p@chrX:1510670..1510699
+
Hg19::chrX:1511254..1511272,+p@chrX:1511254..1511272
+
Hg19::chrX:1511278..1511319,+p@chrX:1511278..1511319
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube6.88e-1456
neural rod6.88e-1456
future spinal cord6.88e-1456
neural keel6.88e-1456
regional part of nervous system3.38e-1253
regional part of brain3.38e-1253
regional part of forebrain6.87e-1141
forebrain6.87e-1141
anterior neural tube6.87e-1141
future forebrain6.87e-1141
brain grey matter2.00e-0934
gray matter2.00e-0934
central nervous system3.60e-0981
female organism1.32e-0841
brain1.52e-0868
future brain1.52e-0868
regional part of telencephalon3.83e-0832
nervous system1.32e-0789
female reproductive organ1.93e-0737
female reproductive system1.93e-0737
neural nucleus2.06e-079
nucleus of brain2.06e-079
ecto-epithelium2.18e-07104
basal ganglion2.40e-079
nuclear complex of neuraxis2.40e-079
aggregate regional part of brain2.40e-079
collection of basal ganglia2.40e-079
cerebral subcortex2.40e-079
telencephalon2.74e-0734
cerebral hemisphere4.31e-0732
neurectoderm7.48e-0786
internal female genitalia9.95e-0722


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)
MA0003.11.54338
MA0004.10.826076
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.13.14798
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.10.714521
MA0060.13.15662
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.13.42881
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.13.21605
MA0106.10.986396
MA0107.11.36919
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
MA0141.14.12088
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
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
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.13.52399
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
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
CCNT2#90536.336201576962630.003930750035764890.0191466630747283
E2F6#187635.017155731697390.00791769806886330.0324854240272643
ELF1#199734.258097958807540.01295179875054610.0465491899139091
ESRRA#21012322.5602094240841.27639599649441e-050.000313217860615318
HNF4G#3174219.16894835096450.003543986611284220.0179814621888803
IRF1#365937.63716375356390.002244692747297240.0128873325180021
NFKB1#479035.488063424193840.006049381815655430.0271027149176457
NFYA#4800212.28372046655370.008516011403724430.0325015061207227
NFYB#4801211.17319550235760.01025467135054530.0381664096496774
NR2C2#7182221.74307393682720.002762207975496010.0151418349124936
NR3C1#290829.982015554115360.01278474365547170.0460867680047567
NRF1#4899312.21027944771090.0005492172401020010.00474007927766407
PAX5#507936.669565531177830.003370290999677260.0173804968257601
PPARGC1A#108912233.3674242424242.43900419981513e-050.000528918520814977
RXRA#6256213.38307809275550.007196434429465730.0298403309397297
SP1#666735.69838137814090.005403962701712170.0248212006598697
THAP1#55145220.91276306856750.002983447413736940.0158795364612818
USF1#739136.361499277207960.00388404057290560.0191414360793549
ZEB1#6935211.25895467836260.01010222676646330.0378295611782954



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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