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Coexpression cluster:C2783: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;10.8437,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;4.37547,MA0014.1;12.5306,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;2.48281,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;2.32784,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;2.526,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;3.49299,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;0.599068,MA0074.1;0.819248,MA0076.1;0.623864,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;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;3.51257,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;1.23748,MA0136.1;0.832277,MA0139.1;0.912459,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.08195,MA0146.1;2.92476,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.10559,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;2.15942,MA0163.1;2.49771,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.657636,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:54, 22 January 2013


Full id: C2783_medulla_optic_blood_Whole_Hepatocyte_substantia_corpus



Phase1 CAGE Peaks

Hg19::chr4:170947459..170947472,-p4@MFAP3L
Hg19::chr4:170947485..170947499,-p2@MFAP3L
Hg19::chr4:170947522..170947563,-p1@MFAP3L
Hg19::chr4:170947565..170947583,-p3@MFAP3L


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
adult organism7.57e-40114
neural tube6.52e-2856
neural rod6.52e-2856
future spinal cord6.52e-2856
neural keel6.52e-2856
nervous system3.41e-2789
central nervous system8.64e-2781
regional part of nervous system3.23e-2653
regional part of brain3.23e-2653
brain1.49e-2268
future brain1.49e-2268
neural plate6.04e-2282
presumptive neural plate6.04e-2282
regional part of forebrain8.19e-2241
forebrain8.19e-2241
anterior neural tube8.19e-2241
future forebrain8.19e-2241
neurectoderm1.00e-2086
telencephalon2.49e-1834
brain grey matter3.29e-1834
gray matter3.29e-1834
pre-chordal neural plate1.80e-1761
ecto-epithelium1.92e-17104
regional part of telencephalon5.05e-1732
cerebral hemisphere5.55e-1732
ectoderm-derived structure2.45e-15171
ectoderm2.45e-15171
presumptive ectoderm2.45e-15171
cerebral cortex7.85e-1325
pallium7.85e-1325
structure with developmental contribution from neural crest2.22e-12132
regional part of cerebral cortex5.60e-1222
neocortex7.68e-1120
organ system subdivision5.05e-10223
tube9.59e-09192
multi-cellular organism4.73e-08656
posterior neural tube2.61e-0715
chordal neural plate2.61e-0715
anatomical conduit5.45e-07240
neural nucleus6.10e-079
nucleus of brain6.10e-079
basal ganglion7.59e-079
nuclear complex of neuraxis7.59e-079
aggregate regional part of brain7.59e-079
collection of basal ganglia7.59e-079
cerebral subcortex7.59e-079
anatomical cluster7.88e-07373


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)
MA0003.110.8437
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.14.37547
MA0014.112.5306
MA0017.10.577281
MA0019.10.873355
MA0024.12.48281
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.12.526
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.13.49299
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.13.51257
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
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.12.92476
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.657636
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#90546.336201576962630.0006203100587215640.00513185695681412
CTCF#1066445.360256373075030.001211145381643620.00819134908130283
E2F1#186944.907389214879320.001724022357361790.0106718332729082
E2F6#187645.017155731697390.00157802193473060.00998588420027442
EGR1#195844.988179094810140.001615011500076050.0101602425189111
ELF1#199744.258097958807540.003041525565781240.0161188353663483
HEY1#2346244.040111043105710.00375304636917980.0186472126427578
IRF1#365947.63716375356390.0002938853996185490.00307978098040956
JUND#372746.994663941871030.000417684217818580.00392253592525444
NRF1#4899412.21027944771094.49717228915276e-050.000794990143376481
PAX5#507946.669565531177830.0005052774169483260.00444646681400962
RAD21#5885410.35503389545638.6948481184721e-050.00129781512454639
SP1#666745.69838137814090.0009482606065333980.00685366017202364
TAF1#687243.343046285745290.008005664898701650.0323019485533728
TCF7L2#6934410.77017656313737.42969445082454e-050.00115658050193719
YY1#752844.911170749853860.00171871838055440.010700520354499



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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