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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0353932040112903,-

Latest revision as of 11:52, 17 September 2013


Full id: C1815_CD4_cerebellum_cord_CD19_pineal_parietal_pituitary



Phase1 CAGE Peaks

Hg19::chr19:19932513..19932569,-p1@ZNF506
Hg19::chr19:19976634..19976677,+p2@ZNF253
Hg19::chr19:20748574..20748599,-p1@ZNF737
Hg19::chr19:22018966..22019001,-p1@ZNF43
Hg19::chr4:331578..331615,+p1@ZNF141


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

p.valueFDRnGenesnPathwayName
4.64055626633526e-102.93747211659022e-075390{ASH2L,391} (Static Module):NA



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:0006355regulation of transcription, DNA-dependent0.000846431334884364
GO:0006351transcription, DNA-dependent0.000846431334884364
GO:0032774RNA biosynthetic process0.000846431334884364
GO:0003677DNA binding0.000846431334884364
GO:0045449regulation of transcription0.000846431334884364
GO:0005730nucleolus0.000846431334884364
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000846431334884364
GO:0006350transcription0.000846431334884364
GO:0010468regulation of gene expression0.000846431334884364
GO:0031323regulation of cellular metabolic process0.000846431334884364
GO:0019222regulation of metabolic process0.000846431334884364
GO:0016070RNA metabolic process0.000846431334884364
GO:0008270zinc ion binding0.000846431334884364
GO:0046914transition metal ion binding0.00151449307368346
GO:0010467gene expression0.00216810207862511
GO:0050794regulation of cellular process0.00243180912712297
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00252885068474743
GO:0005634nucleus0.00274969000691553
GO:0050789regulation of biological process0.00274969000691553
GO:0003676nucleic acid binding0.00303959206670695
GO:0043169cation binding0.00311902856622841
GO:0065007biological regulation0.00343002124051222
GO:0046872metal ion binding0.00350277187617976
GO:0043167ion binding0.00359037836362785
GO:0031981nuclear lumen0.0047146401294312
GO:0043283biopolymer metabolic process0.00562041980758463
GO:0043231intracellular membrane-bound organelle0.00744887228320251
GO:0043227membrane-bound organelle0.00744887228320251
GO:0003704specific RNA polymerase II transcription factor activity0.00744887228320251
GO:0031974membrane-enclosed lumen0.00744887228320251
GO:0043233organelle lumen0.00744887228320251
GO:0044428nuclear part0.0093458991010516
GO:0043229intracellular organelle0.0145414453986348
GO:0043226organelle0.0145414453986348
GO:0043170macromolecule metabolic process0.016205067423626
GO:0044237cellular metabolic process0.026309483769755
GO:0044238primary metabolic process0.026383330268527
GO:0044424intracellular part0.0272869829045711
GO:0016564transcription repressor activity0.0313615375688903
GO:0003702RNA polymerase II transcription factor activity0.0397506666735284
GO:0005622intracellular0.0442867803553934
GO:0043232intracellular non-membrane-bound organelle0.0448997808200877
GO:0043228non-membrane-bound organelle0.0448997808200877



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 organism9.28e-29114
nervous system1.02e-2189
central nervous system8.69e-2181
neural tube6.64e-2056
neural rod6.64e-2056
future spinal cord6.64e-2056
neural keel6.64e-2056
regional part of nervous system1.22e-1853
regional part of brain1.22e-1853
regional part of forebrain5.00e-1741
forebrain5.00e-1741
anterior neural tube5.00e-1741
future forebrain5.00e-1741
neurectoderm6.63e-1786
brain7.56e-1668
future brain7.56e-1668
neural plate9.08e-1682
presumptive neural plate9.08e-1682
brain grey matter1.71e-1334
gray matter1.71e-1334
telencephalon2.10e-1334
pre-chordal neural plate3.04e-1361
regional part of telencephalon7.03e-1332
cerebral hemisphere1.29e-1232
ecto-epithelium2.83e-11104
ectoderm-derived structure2.87e-11171
ectoderm2.87e-11171
presumptive ectoderm2.87e-11171
cerebral cortex8.40e-1025
pallium8.40e-1025
regional part of cerebral cortex9.86e-1022
neocortex7.36e-0920
structure with developmental contribution from neural crest2.94e-08132
blood7.79e-0715
haemolymphatic fluid7.79e-0715
organism substance7.79e-0715


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)
MA0003.10.136928
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.13.05902
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.11.29682
MA0060.15.26847
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.13.37477
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.11.25946
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.11.35428
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.23.02043
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.83106
MA0137.21.20193
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.21.83842
MA0099.20.699641
MA0079.20.00732454
MA0102.21.66336
MA0258.10.914277
MA0259.11.02361
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
CHD2#110636.206413700470110.007774550126275590.0319558518886259
ELF1#199754.258097958807540.0007142416939776840.00573232062378663
FOS#235358.99795530889441.69470025615156e-050.000389166227027733
GATA2#2624410.19594538684320.0001775447777609820.00215711947936007
GATA3#2625316.34190981432360.0004678865195089230.00430192800519345
IRF3#3661328.18917132689379.33088977565955e-050.00135631008668073
NFYA#4800414.74046455986444.14733626928016e-050.000752246704806096
NFYB#4801413.40783460282926.03169250119439e-050.00099141317773409
PBX3#5090313.14870761204650.0008860469322808430.00660371480485827
POU2F2#545247.284899246194020.0006631223288743860.00542587221132184
SP1#666755.69838137814090.000166391843712550.00204324488718342
SP2#6668210.46141219753790.01353191183347140.0477823761698589
TAF1#687253.343046285745290.002394600090870310.0135395830702401
TAF7#687949.146455523939130.0002720662872412990.00290297619260258
TBP#690853.706770687096390.001428755106721120.009189417082821



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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