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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:34, 17 September 2013


Full id: C931_neuroectodermal_peripheral_maxillary_gastrointestinal_Hepatocyte_small_liver



Phase1 CAGE Peaks

Hg19::chr1:214160884..214160892,-p@chr1:214160884..214160892
-
Hg19::chr1:214161272..214161322,+p1@PROX1
Hg19::chr1:214161328..214161348,+p2@PROX1
Hg19::chr1:214161358..214161377,+p3@PROX1
Hg19::chr1:214161428..214161437,+p6@PROX1
Hg19::chr1:214170889..214170891,+p@chr1:214170889..214170891
+
Hg19::chr1:214171294..214171305,+p@chr1:214171294..214171305
+
Hg19::chr1:214175769..214175774,+p@chr1:214175769..214175774
+
Hg19::chr1:214214418..214214425,+p@chr1:214214418..214214425
+


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 tube1.87e-3456
neural rod1.87e-3456
future spinal cord1.87e-3456
neural keel1.87e-3456
adult organism8.17e-33114
regional part of nervous system2.35e-3153
regional part of brain2.35e-3153
neurectoderm2.16e-3086
nervous system2.63e-2989
central nervous system3.52e-2881
neural plate6.91e-2882
presumptive neural plate6.91e-2882
brain9.57e-2768
future brain9.57e-2768
regional part of forebrain1.21e-2641
forebrain1.21e-2641
anterior neural tube1.21e-2641
future forebrain1.21e-2641
telencephalon1.23e-2234
brain grey matter1.28e-2234
gray matter1.28e-2234
organ system subdivision2.02e-21223
ecto-epithelium5.05e-21104
regional part of telencephalon1.27e-2032
pre-chordal neural plate1.55e-2061
cerebral hemisphere2.30e-2032
structure with developmental contribution from neural crest1.99e-17132
anatomical cluster3.18e-17373
regional part of cerebral cortex1.24e-1622
ectoderm-derived structure1.37e-16171
ectoderm1.37e-16171
presumptive ectoderm1.37e-16171
neocortex3.08e-1420
cerebral cortex4.95e-1425
pallium4.95e-1425
tube7.41e-14192
anatomical conduit7.92e-13240
neural nucleus1.08e-109
nucleus of brain1.08e-109
epithelium1.34e-10306
cell layer2.78e-10309
multi-tissue structure2.43e-09342
posterior neural tube6.71e-0915
chordal neural plate6.71e-0915
telencephalic nucleus1.28e-087
basal ganglion2.10e-089
nuclear complex of neuraxis2.10e-089
aggregate regional part of brain2.10e-089
collection of basal ganglia2.10e-089
cerebral subcortex2.10e-089
multi-cellular organism1.42e-07656
brainstem1.53e-076
segmental subdivision of nervous system3.06e-0713
anatomical system5.22e-07624
embryo5.95e-07592
anatomical group6.05e-07625
organ part9.27e-07218


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)
MA0003.10.169975
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.12.31793
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.11.95759
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.12.4985
MA0058.10.325084
MA0059.10.323879
MA0060.10.9464
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.719601
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.116.0786
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.13.05179
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.24.09994
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.11.19454
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.319685
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.21.7915
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.674448
MA0065.20.408099
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.27.18108
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
CTBP2#1488427.87422237303477.62341479845092e-060.000217417208666143
FOXA1#316978.61888202729981.48686672954246e-065.7322581899847e-05
FOXA2#3170719.15702736318416.07362166732378e-094.816423487575e-07



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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