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{{Coexpression_clusters
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|full_id=C4823_signet_tubular_Smooth_small_Hepatocyte_Fibroblast_Sertoli
|id=C4823
|ontology_enrichment_celltype=CL:0000359!1.35e-12!32;CL:0000192!2.27e-10!42;CL:0000514!2.27e-10!42;CL:0000055!3.06e-10!180;CL:0000680!8.07e-09!57;CL:0000056!8.07e-09!57;CL:0000355!8.07e-09!57;CL:0000393!3.37e-08!60;CL:0000211!3.37e-08!60;CL:0000187!6.73e-08!54;CL:0000222!9.67e-08!119;CL:0002334!3.40e-07!12;CL:0000183!3.65e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000025!1.62e-24!194;UBERON:0000477!2.20e-23!286;UBERON:0004111!2.35e-23!241;UBERON:0000483!5.67e-19!309;UBERON:0000119!1.94e-18!312;UBERON:0000475!6.58e-18!365;UBERON:0000481!2.34e-17!347;UBERON:0001637!4.45e-16!42;UBERON:0003509!4.45e-16!42;UBERON:0004572!4.45e-16!42;UBERON:0003914!4.87e-15!118;UBERON:0004573!6.45e-14!33;UBERON:0004571!6.45e-14!33;UBERON:0001981!3.13e-13!60;UBERON:0007500!3.13e-13!60;UBERON:0004537!3.13e-13!60;UBERON:0006965!3.13e-13!60;UBERON:0002049!6.44e-13!79;UBERON:0007798!6.44e-13!79;UBERON:0000055!8.38e-13!69;UBERON:0000490!1.27e-12!138;UBERON:0004872!1.36e-12!84;UBERON:0001017!1.01e-11!82;UBERON:0001049!1.29e-11!57;UBERON:0005068!1.29e-11!57;UBERON:0006241!1.29e-11!57;UBERON:0007135!1.29e-11!57;UBERON:0002616!1.83e-11!59;UBERON:0002780!2.25e-11!41;UBERON:0001890!2.25e-11!41;UBERON:0006240!2.25e-11!41;UBERON:0000468!3.82e-11!659;UBERON:0005743!4.24e-11!86;UBERON:0003080!4.29e-11!42;UBERON:0002619!7.78e-11!22;UBERON:0001869!8.19e-11!32;UBERON:0000073!8.77e-11!94;UBERON:0001016!8.77e-11!94;UBERON:0001893!9.22e-11!34;UBERON:0002100!1.10e-10!216;UBERON:0002020!1.25e-10!34;UBERON:0003528!1.25e-10!34;UBERON:0000955!1.69e-10!69;UBERON:0006238!1.69e-10!69;UBERON:0002791!2.59e-10!33;UBERON:0005256!3.77e-10!143;UBERON:0001950!5.40e-10!20;UBERON:0000480!1.45e-09!626;UBERON:0000467!1.60e-09!625;UBERON:0002346!1.92e-09!90;UBERON:0003075!2.27e-09!86;UBERON:0007284!2.27e-09!86;UBERON:0002385!1.97e-08!63;UBERON:0001015!1.97e-08!63;UBERON:0000383!1.97e-08!63;UBERON:0000956!2.42e-08!25;UBERON:0000203!2.42e-08!25;UBERON:0003056!3.71e-08!61;UBERON:0004535!4.11e-08!110;UBERON:0001009!4.97e-08!113;UBERON:0007023!5.53e-08!115;UBERON:0001134!9.59e-08!61;UBERON:0002036!9.59e-08!61;UBERON:0003082!9.59e-08!61;UBERON:0000922!9.68e-08!612;UBERON:0000947!1.19e-07!21;UBERON:0010191!1.19e-07!21;UBERON:0002050!1.36e-07!605;UBERON:0005423!1.36e-07!605;UBERON:0000923!1.75e-07!604;UBERON:0005291!1.75e-07!604;UBERON:0006598!1.75e-07!604;UBERON:0002532!1.75e-07!604;UBERON:0000914!1.89e-07!83;UBERON:0002329!1.89e-07!83;UBERON:0003077!1.89e-07!83;UBERON:0003059!1.89e-07!83;UBERON:0007282!1.89e-07!83;UBERON:0009618!1.89e-07!83;UBERON:0007285!1.89e-07!83;UBERON:0000033!4.33e-07!123
}}

Latest revision as of 14:20, 17 September 2013


Full id: C4823_signet_tubular_Smooth_small_Hepatocyte_Fibroblast_Sertoli



Phase1 CAGE Peaks

Hg19::chr9:4490394..4490446,+p2@SLC1A1
Hg19::chr9:4490449..4490481,+p1@SLC1A1
Hg19::chr9:4490482..4490518,+p3@SLC1A1


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
anatomical cluster9.67e-28373
tube7.60e-25192
anatomical conduit9.11e-24240
epithelium1.11e-19306
cell layer3.74e-19309
multi-tissue structure2.59e-17342
artery4.71e-1642
arterial blood vessel4.71e-1642
arterial system4.71e-1642
epithelial tube9.21e-16117
systemic artery9.98e-1433
systemic arterial system9.98e-1433
epithelial tube open at both ends2.91e-1359
blood vessel2.91e-1359
blood vasculature2.91e-1359
vascular cord2.91e-1359
splanchnic layer of lateral plate mesoderm4.18e-1383
vasculature5.00e-1378
vascular system5.00e-1378
vessel5.40e-1368
structure with developmental contribution from neural crest6.81e-12132
unilaminar epithelium7.35e-12148
central nervous system2.26e-1181
neural tube3.79e-1156
neural rod3.79e-1156
future spinal cord3.79e-1156
neural keel3.79e-1156
nervous system5.35e-1189
cerebral hemisphere6.15e-1132
telencephalon9.25e-1134
multi-cellular organism9.45e-11656
regional part of forebrain9.55e-1141
forebrain9.55e-1141
anterior neural tube9.55e-1141
future forebrain9.55e-1141
regional part of cerebral cortex9.87e-1122
brain grey matter1.12e-1034
gray matter1.12e-1034
regional part of nervous system1.29e-1053
regional part of brain1.29e-1053
regional part of telencephalon2.09e-1032
organ system subdivision2.83e-10223
brain6.12e-1068
future brain6.12e-1068
neocortex6.57e-1020
anatomical group6.80e-10625
anatomical system7.49e-10624
neural plate1.05e-0982
presumptive neural plate1.05e-0982
neurectoderm1.34e-0986
mesenchyme1.80e-09160
entire embryonic mesenchyme1.80e-09160
cerebral cortex1.98e-0825
pallium1.98e-0825
cardiovascular system2.01e-08109
pre-chordal neural plate2.16e-0861
circulatory system2.61e-08112
muscle tissue2.74e-0864
musculature2.74e-0864
musculature of body2.74e-0864
trunk2.94e-08199
skeletal muscle tissue1.51e-0762
striated muscle tissue1.51e-0762
myotome1.51e-0762
aorta1.52e-0721
aortic system1.52e-0721
trunk mesenchyme2.11e-07122
adult organism2.74e-07114
organism subdivision3.12e-07264
embryo4.89e-07592
developing anatomical structure7.59e-07581
dense mesenchyme tissue8.72e-0773


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)
MA0003.10.708947
MA0004.10.826076
MA0006.13.80603
MA0007.11.88666
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.13.54769
MA0052.11.24796
MA0055.111.1527
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
E2F1#186934.907389214879320.008460985347239390.0328228530079613
EBF1#187938.9064668465690.00141523283560980.00919760436330133
EGR1#195834.988179094810140.008056488137383440.0322911910266028
ZNF263#1012738.221841637010680.001799043925565870.0110270760339324



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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