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{{Coexpression_clusters
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|full_id=C2605_Reticulocytes_liver_Hepatocyte_retina_left_heart_gastrointestinal
|id=C2605
}}

Latest revision as of 12:09, 17 September 2013


Full id: C2605_Reticulocytes_liver_Hepatocyte_retina_left_heart_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr1:95582881..95582994,+p1@TMEM56
Hg19::chr1:95583232..95583264,+p3@RWDD3
p3@TMEM56
Hg19::chr3:142682505..142682521,-p2@PAQR9
Hg19::chr7:100239132..100239196,-p3@TFR2


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:0004998transferrin receptor activity0.00865393104790558



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism1.07e-52114
organ system subdivision5.43e-33223
neural tube9.89e-3256
neural rod9.89e-3256
future spinal cord9.89e-3256
neural keel9.89e-3256
regional part of nervous system6.81e-3053
regional part of brain6.81e-3053
central nervous system1.36e-2981
neural plate7.90e-2982
presumptive neural plate7.90e-2982
brain2.92e-2868
future brain2.92e-2868
regional part of forebrain1.00e-2741
forebrain1.00e-2741
anterior neural tube1.00e-2741
future forebrain1.00e-2741
nervous system6.47e-2789
neurectoderm2.64e-2686
telencephalon3.04e-2534
brain grey matter6.92e-2534
gray matter6.92e-2534
cerebral hemisphere3.71e-2432
pre-chordal neural plate6.16e-2461
regional part of telencephalon7.04e-2432
ecto-epithelium1.38e-20104
anatomical cluster2.12e-20373
regional part of cerebral cortex1.38e-1922
cerebral cortex1.53e-1825
pallium1.53e-1825
structure with developmental contribution from neural crest2.23e-18132
neocortex5.26e-1820
multi-tissue structure4.85e-17342
ectoderm-derived structure1.52e-15171
ectoderm1.52e-15171
presumptive ectoderm1.52e-15171
organ part6.43e-12218
tube2.08e-11192
anatomical conduit4.26e-11240
subdivision of digestive tract1.12e-10118
organ2.90e-10503
digestive system1.60e-08145
digestive tract1.60e-08145
primitive gut1.60e-08145
embryo2.01e-08592
basal ganglion2.41e-089
nuclear complex of neuraxis2.41e-089
aggregate regional part of brain2.41e-089
collection of basal ganglia2.41e-089
cerebral subcortex2.41e-089
epithelium7.46e-08306
neural nucleus8.80e-089
nucleus of brain8.80e-089
developing anatomical structure1.57e-07581
cell layer1.70e-07309
temporal lobe7.16e-076
telencephalic nucleus7.83e-077
endoderm-derived structure8.84e-07160
endoderm8.84e-07160
presumptive endoderm8.84e-07160
Disease
Ontology termp-valuen
carcinoma3.55e-08106


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)
MA0003.12.92335
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.12.02743
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.12.64938
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
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
MA0101.11.33363
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.11.15856
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
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.6798
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#90546.336201576962630.0006203100587215640.00512617203852045
E2F6#187645.017155731697390.00157802193473060.00997621264172694
HEY1#2346244.040111043105710.00375304636917980.0186250610477914
HMGN3#932436.133910792512940.006640696683324720.0283011393499449
TAF1#687243.343046285745290.008005664898701650.0322558402976545
ZBTB7A#5134135.513931980906920.009038352821081090.0342509626371875



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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