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{{Coexpression_clusters
{
|full_id=C2654_Chondrocyte_Renal_Fibroblast_Anulus_sacrococcigeal_Smooth_Osteoblast

Latest revision as of 12:10, 17 September 2013


Full id: C2654_Chondrocyte_Renal_Fibroblast_Anulus_sacrococcigeal_Smooth_Osteoblast



Phase1 CAGE Peaks

Hg19::chr2:106015446..106015457,-p4@FHL2
Hg19::chr2:106015472..106015488,-p2@FHL2
Hg19::chr2:106015491..106015518,-p1@FHL2
Hg19::chr2:106015527..106015538,-p6@FHL2


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>

Uber Anatomy
Ontology termp-valuen
organism subdivision1.27e-19264
mesenchyme6.95e-18160
entire embryonic mesenchyme6.95e-18160
trunk6.06e-17199
vasculature1.84e-1678
vascular system1.84e-1678
epithelial vesicle2.15e-1678
epithelial tube1.13e-15117
multilaminar epithelium1.39e-1583
unilaminar epithelium2.03e-15148
somite5.08e-1571
presomitic mesoderm5.08e-1571
presumptive segmental plate5.08e-1571
dermomyotome5.08e-1571
trunk paraxial mesoderm5.08e-1571
dense mesenchyme tissue8.18e-1573
paraxial mesoderm1.26e-1472
presumptive paraxial mesoderm1.26e-1472
skeletal muscle tissue1.48e-1462
striated muscle tissue1.48e-1462
myotome1.48e-1462
trunk mesenchyme1.70e-14122
muscle tissue2.46e-1464
musculature2.46e-1464
musculature of body2.46e-1464
artery6.27e-1342
arterial blood vessel6.27e-1342
arterial system6.27e-1342
splanchnic layer of lateral plate mesoderm8.80e-1383
epithelial tube open at both ends1.18e-1259
blood vessel1.18e-1259
blood vasculature1.18e-1259
vascular cord1.18e-1259
vessel3.63e-1268
multi-tissue structure1.19e-11342
multi-cellular organism3.80e-11656
cell layer4.35e-11309
anatomical cluster1.24e-10373
systemic artery1.75e-1033
systemic arterial system1.75e-1033
epithelium2.11e-10306
cardiovascular system2.91e-10109
surface structure9.19e-1099
anatomical system1.04e-09624
circulatory system1.09e-09112
anatomical group1.66e-09625
organ component layer3.77e-0766


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)
MA0003.16.84463
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
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
MA0038.10.824639
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
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.36824
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.110.0819
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.14.42006
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.13.57466
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
MA0146.19.23949
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.12.59564
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.13.05999
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.12283
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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#90546.336201576962630.0006203100587215640.00512738917473854
CTCF#1066445.360256373075030.001211145381643620.0081812827445494
CTCFL#140690419.74647435897446.5732084880439e-060.000193162442679464
E2F1#186944.907389214879320.001724022357361790.0106604600935765
E2F4#1874412.66806031528443.88145892637771e-050.000727653363510971
E2F6#187645.017155731697390.00157802193473060.00997802463167215
ELF1#199744.258097958807540.003041525565781240.0161073925543647
ELK4#2005416.2356816584681.43847748454449e-050.000343468564262327
EP300#203346.77394172622320.0004748459821442640.00434525887401777
HEY1#2346244.040111043105710.00375304636917980.0186321438299553
HMGN3#932448.178547723350590.0002234570284440470.00248325479821961
JUND#372746.994663941871030.000417684217818580.00392042078051179
MAFF#23764228.15767824497260.001846876180367150.0109265224835079
NANOG#79923429.24477848101271.36586687657858e-065.34268804205957e-05
NRF1#4899412.21027944771094.49717228915276e-050.000794452261006132
PAX5#507946.669565531177830.0005052774169483260.004443471551757
RAD21#5885410.35503389545638.6948481184721e-050.00129559315543602
SETDB1#9869440.32002617801053.77887289069054e-071.85200237367822e-05
SRF#6722413.79717826216782.75840773062708e-050.000585063657552724
TAF1#687243.343046285745290.008005664898701650.0322682890029525
TAF7#6879411.43306940492395.85061525419808e-050.00097050890491295
TBP#690843.706770687096390.005296377814784350.0244582774406731
ZBTB7A#5134147.35190930787590.000342223540015990.00346937335427392
ZNF263#1012736.166381227758010.006539814347975980.0279796678009202



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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