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{{Coexpression_clusters
{
|full_id=C891_Fibroblast_occipital_mesothelioma_cholangiocellular_neuroblastoma_pineal_hippocampus

Latest revision as of 11:33, 17 September 2013


Full id: C891_Fibroblast_occipital_mesothelioma_cholangiocellular_neuroblastoma_pineal_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:130303291..130303304,-p@chr12:130303291..130303304
-
Hg19::chr5:167000419..167000430,+p@chr5:167000419..167000430
+
Hg19::chr5:167000441..167000460,+p@chr5:167000441..167000460
+
Hg19::chr5:167000581..167000611,+p6@ODZ2
Hg19::chr5:167000625..167000675,+p5@ODZ2
Hg19::chr5:167000685..167000706,+p11@ODZ2
Hg19::chr5:167000707..167000719,+p16@ODZ2
Hg19::chr5:167000959..167001019,+p2@ODZ2
Hg19::chr5:167148342..167148357,+p1@ENST00000517346


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>disease_data<br>

Cell Type
Ontology termp-valuen
skin fibroblast1.00e-1123
Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.67e-4553
regional part of brain6.67e-4553
neural tube2.98e-4456
neural rod2.98e-4456
future spinal cord2.98e-4456
neural keel2.98e-4456
regional part of forebrain3.42e-4141
forebrain3.42e-4141
anterior neural tube3.42e-4141
future forebrain3.42e-4141
central nervous system8.97e-4081
cerebral hemisphere1.38e-3932
brain grey matter2.84e-3934
gray matter2.84e-3934
telencephalon3.54e-3934
nervous system4.98e-3889
brain1.13e-3768
future brain1.13e-3768
regional part of cerebral cortex2.17e-3722
regional part of telencephalon1.67e-3632
neurectoderm2.04e-3686
neocortex7.99e-3420
neural plate1.35e-3382
presumptive neural plate1.35e-3382
cerebral cortex3.52e-3225
pallium3.52e-3225
pre-chordal neural plate6.93e-3161
ecto-epithelium1.05e-24104
ectoderm-derived structure4.79e-23171
ectoderm4.79e-23171
presumptive ectoderm4.79e-23171
structure with developmental contribution from neural crest1.06e-21132
adult organism5.22e-18114
organ system subdivision6.66e-13223
gyrus7.99e-126
occipital lobe1.56e-105
temporal lobe4.81e-106
limbic system5.01e-105
parietal lobe5.69e-105
basal ganglion4.50e-099
nuclear complex of neuraxis4.50e-099
aggregate regional part of brain4.50e-099
collection of basal ganglia4.50e-099
cerebral subcortex4.50e-099
organ4.61e-09503
tube6.79e-09192
neural nucleus1.14e-089
nucleus of brain1.14e-089
corpus striatum9.10e-084
striatum9.10e-084
ventral part of telencephalon9.10e-084
future corpus striatum9.10e-084
organ part3.92e-07218
anatomical cluster4.07e-07373
brainstem6.95e-076
Disease
Ontology termp-valuen
musculoskeletal system disease2.19e-085
myotonic disease2.19e-085
muscle tissue disease2.19e-085
myopathy2.19e-085
muscular disease2.19e-085
myotonic dystrophy2.19e-085


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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
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
MA0038.12.20905
MA0040.10.791764
MA0041.10.433167
MA0042.11.03929
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.11.04113
MA0051.11.27173
MA0052.10.795605
MA0055.12.85007
MA0056.10
MA0057.10.919325
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.11.94461
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.12.6472
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
MA0108.20.707575
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
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.21.45266
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.408099
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.101664
MA0164.10.583138
MA0080.20.268439
MA0018.21.36887
MA0099.20.481058
MA0079.20.0681378
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
CTCF#1066463.573504248716680.002103883629372150.0121658547349537
TAF7#687945.081364179966180.00514192961203820.023905715222207



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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