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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:41, 17 September 2013


Full id: C1251_adipose_heart_left_trachea_dura_cervix_bladder



Phase1 CAGE Peaks

Hg19::chr1:159174510..159174521,+p5@DARC
Hg19::chr1:159174575..159174586,+p4@DARC
Hg19::chr1:159174623..159174628,+p6@DARC
Hg19::chr1:159174649..159174700,+p1@DARC
Hg19::chr1:159174701..159174727,+p2@DARC
Hg19::chr1:159175250..159175264,+p9@DARC
Hg19::chr3:64673656..64673667,-p3@ADAMTS9


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

GO IDGO nameFDR corrected p-value
GO:0006516glycoprotein catabolic process0.0273899974692192
GO:0001637G-protein chemoattractant receptor activity0.0273899974692192
GO:0004950chemokine receptor activity0.0273899974692192
GO:0019956chemokine binding0.0273899974692192



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 organism2.87e-90114
neural tube3.63e-2856
neural rod3.63e-2856
future spinal cord3.63e-2856
neural keel3.63e-2856
regional part of nervous system2.87e-2453
regional part of brain2.87e-2453
neural plate5.11e-2382
presumptive neural plate5.11e-2382
neurectoderm2.01e-2186
central nervous system3.73e-2081
regional part of forebrain1.20e-1841
forebrain1.20e-1841
anterior neural tube1.20e-1841
future forebrain1.20e-1841
nervous system1.81e-1889
brain5.06e-1868
future brain5.06e-1868
structure with developmental contribution from neural crest8.58e-18132
ecto-epithelium7.41e-17104
brain grey matter5.03e-1634
gray matter5.03e-1634
telencephalon9.67e-1634
organ system subdivision1.72e-15223
regional part of telencephalon1.09e-1332
cerebral hemisphere2.48e-1332
anatomical cluster6.58e-13373
pre-chordal neural plate8.88e-1361
multi-tissue structure1.79e-11342
brainstem3.50e-116
regional part of cerebral cortex5.41e-1122
posterior neural tube6.85e-1115
chordal neural plate6.85e-1115
ectoderm-derived structure1.75e-10171
ectoderm1.75e-10171
presumptive ectoderm1.75e-10171
anatomical conduit2.25e-10240
neocortex2.43e-1020
cerebral cortex2.42e-0925
pallium2.42e-0925
tube3.63e-09192
basal ganglion4.66e-099
nuclear complex of neuraxis4.66e-099
aggregate regional part of brain4.66e-099
collection of basal ganglia4.66e-099
cerebral subcortex4.66e-099
neural nucleus4.72e-099
nucleus of brain4.72e-099
organ1.13e-08503
temporal lobe1.56e-086
segmental subdivision of nervous system2.51e-0813
organ part1.06e-07218
regional part of diencephalon1.09e-074
cardiac chamber2.39e-073
compound organ6.09e-0768
medulla oblongata6.44e-073
myelencephalon6.44e-073
future myelencephalon6.44e-073
segmental subdivision of hindbrain6.65e-0712
hindbrain6.65e-0712
presumptive hindbrain6.65e-0712


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)
MA0003.10.358813
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.15.93671
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.11.39306
MA0072.10.942461
MA0073.10.215865
MA0074.12.49417
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.17.81405
MA0103.10.332048
MA0105.11.14871
MA0106.10.648997
MA0107.16.93231
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.11.59862
MA0114.12.09327
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.04496
MA0140.14.68258
MA0141.11.83545
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.11.36656
MA0062.20.193221
MA0035.22.37179
MA0039.20.243958
MA0138.20.704862
MA0002.20.213296
MA0137.20.95459
MA0104.20.223944
MA0047.20.636643
MA0112.20.944394
MA0065.22.03906
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.942271
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.263996
MA0102.21.51913
MA0258.10.687127
MA0259.10.787775
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
GATA1#262359.685934388428894.03236593682386e-050.000738835554519206
NFKB1#479053.92004530299560.003036581424484610.0161212651175146
POLR2A#543072.147453176558070.004747636447610280.0223501646586419
REST#597868.271453185252597.89289295030691e-060.000222850999415275
TAL1#6886417.06778095853734.05034184451705e-050.000741218944979002



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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