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Coexpression cluster:C2756: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2756_skeletal_Adipocyte_mature_Preadipocyte_Hepatic_Mesenchymal_aorta
|id=C2756
}}

Latest revision as of 12:12, 17 September 2013


Full id: C2756_skeletal_Adipocyte_mature_Preadipocyte_Hepatic_Mesenchymal_aorta



Phase1 CAGE Peaks

Hg19::chr3:8543500..8543518,+p1@LMCD1
Hg19::chr3:8543533..8543553,+p2@LMCD1
Hg19::chr3:8543561..8543579,+p3@LMCD1
Hg19::chr3:8543591..8543602,+p4@LMCD1


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><br>

Cell Type
Ontology termp-valuen
fat cell5.84e-0915
fibroblast3.95e-0776
Uber Anatomy
Ontology termp-valuen
organism subdivision6.52e-14264
trunk8.71e-13199
mesenchyme3.54e-12160
entire embryonic mesenchyme3.54e-12160
epithelium8.53e-12306
cell layer1.03e-11309
multi-tissue structure9.48e-11342
multi-cellular organism1.62e-10656
compound organ2.69e-1068
trunk mesenchyme1.84e-08122
subdivision of trunk2.77e-08112
epithelial tube5.55e-08117
anatomical cluster1.83e-07373
anatomical conduit2.41e-07240
primary circulatory organ2.42e-0727
adipose tissue2.52e-0714
tube4.70e-07192
epithelial vesicle7.18e-0778


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.15.64565
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.13.69367
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
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
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.12.66544
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
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
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.13.19603
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.22.1393
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.23.34398
MA0099.20.7872
MA0079.20.327251
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
CHD2#1106410.34402283411698.73193255208051e-050.00129226909991035
CTCF#1066445.360256373075030.001211145381643620.00818869764442793
E2F1#186944.907389214879320.001724022357361790.0106674074874405
E2F6#187645.017155731697390.00157802193473060.00998406935489968
FOS#235348.99795530889440.0001525147711168630.00195178166654504
HEY1#2346244.040111043105710.00375304636917980.018643664847354
MAFF#23764228.15767824497260.001846876180367150.0109271414797963
MAX#414946.452555509007120.0005767613195645490.00486090828389299
MYC#460945.22228187160940.001344309395272740.00888822036799755
NFYA#4800418.42558069983058.67100748407158e-060.000234913450228003
NFYB#4801416.75979325353651.26678572070404e-050.000311738534129617
NRF1#4899412.21027944771094.49717228915276e-050.000794855604513158
PAX5#507946.669565531177830.0005052774169483260.00444609218541294
RFX5#5993412.04791082719514.74457429336527e-050.000827657582469977
SETDB1#9869440.32002617801053.77887289069054e-071.8528718583607e-05
SP1#666745.69838137814090.0009482606065333980.00685271169981605
SP2#6668426.15353049384462.13562021071447e-067.75528648076526e-05
SRF#6722413.79717826216782.75840773062708e-050.000585182500465084
TAF1#687243.343046285745290.008005664898701650.032294462586153
TCF7L2#6934410.77017656313737.42969445082454e-050.00115623581992201
YY1#752844.911170749853860.00171871838055440.0106992447366467
ZNF263#1012748.221841637010680.0002187871180958320.00249562121306363



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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