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{{Coexpression_clusters
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|full_id=C4641_mature_breast_Whole_Burkitt_pineal_adipose_chronic
|id=C4641
}}

Latest revision as of 14:16, 17 September 2013


Full id: C4641_mature_breast_Whole_Burkitt_pineal_adipose_chronic



Phase1 CAGE Peaks

Hg19::chr7:106685105..106685126,+p2@PRKAR2B
Hg19::chr7:106685133..106685186,+p1@PRKAR2B
Hg19::chr7:106685220..106685231,+p4@PRKAR2B


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.46e-37114
central nervous system5.53e-2381
neural tube7.40e-2256
neural rod7.40e-2256
future spinal cord7.40e-2256
neural keel7.40e-2256
nervous system2.49e-2189
regional part of nervous system2.63e-2153
regional part of brain2.63e-2153
regional part of forebrain3.46e-2041
forebrain3.46e-2041
anterior neural tube3.46e-2041
future forebrain3.46e-2041
brain4.31e-1868
future brain4.31e-1868
neural plate3.68e-1782
presumptive neural plate3.68e-1782
neurectoderm4.80e-1786
telencephalon8.31e-1734
cerebral hemisphere9.88e-1732
brain grey matter1.12e-1634
gray matter1.12e-1634
regional part of telencephalon3.38e-1632
pre-chordal neural plate1.20e-1461
regional part of cerebral cortex9.48e-1422
neocortex3.35e-1320
cerebral cortex3.38e-1325
pallium3.38e-1325
organ system subdivision4.19e-11223
structure with developmental contribution from neural crest1.93e-09132
ectoderm-derived structure2.30e-09171
ectoderm2.30e-09171
presumptive ectoderm2.30e-09171
anatomical cluster2.99e-09373
ecto-epithelium3.06e-08104
tissue1.54e-07773
blood vessel endothelium4.65e-0718
endothelium4.65e-0718
cardiovascular system endothelium4.65e-0718


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)
MA0003.13.8806
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.16.45108
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.886807
MA0058.14.13609
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
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.13.82193
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
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.12.91906
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.25.75024
MA0065.20.760954
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
MA0162.14.34338
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.90173
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
ATF3#467322.46317452600878.81932387510763e-050.00130022778965608
CCNT2#90536.336201576962630.003930750035764890.0191074518494414
CHD2#1106310.34402283411690.0009033701102746880.00662689267029417
CTCF#1066435.360256373075030.0064925092527670.0281182323802502
E2F1#186934.907389214879320.008460985347239390.032755934636184
E2F4#1874312.66806031528440.0004917987006298980.00438849662466558
E2F6#187635.017155731697390.00791769806886330.0324179264785171
EGR1#195834.988179094810140.008056488137383440.0322367558553385
ELF1#199734.258097958807540.01295179875054610.0464804106146754
EP300#203336.77394172622320.003216880500103790.016838802252924
HDAC2#3066313.41562023662630.0004140761399857210.00393393049976974
HMGN3#932438.178547723350590.001827766942164210.0109161177830782
IRF1#365937.63716375356390.002244692747297240.0128703522281074
JUND#372736.994663941871030.002921845042734990.0157637449332679
MAX#414936.452555509007120.003721913834265510.0187349604268775
MXI1#460139.96157162875930.001011470541259020.00723194166211755
NRF1#4899312.21027944771090.0005492172401020010.00473303897508152
RAD21#5885310.35503389545630.0009004912073565420.00668227946604447
SIN3A#2594235.408884726815140.006318961977991520.027820001265469
USF1#739136.361499277207960.00388404057290560.0191107751528167
USF2#7392312.99219738506960.0004558979393427810.00423080903563362
YY1#752834.911170749853860.008441455341808260.0331111377767262



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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