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{{Coexpression_clusters
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|full_id=C3902_Hepatocyte_liver_hepatoma_Neutrophils_medulla_placenta_CD4
|id=C3902
}}

Latest revision as of 12:35, 17 September 2013


Full id: C3902_Hepatocyte_liver_hepatoma_Neutrophils_medulla_placenta_CD4



Phase1 CAGE Peaks

Hg19::chr1:169555677..169555678,-p4@F5
Hg19::chr1:169555684..169555705,-p2@F5
Hg19::chr1:169555709..169555730,-p1@F5


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
classical monocyte3.66e-2742
CD14-positive, CD16-negative classical monocyte3.66e-2742
myeloid leukocyte7.84e-2672
leukocyte3.28e-22136
defensive cell1.13e-2148
phagocyte1.13e-2148
myeloid lineage restricted progenitor cell1.17e-1966
granulocyte monocyte progenitor cell2.55e-1867
monopoietic cell3.92e-1859
monocyte3.92e-1859
monoblast3.92e-1859
promonocyte3.92e-1859
nongranular leukocyte5.91e-18115
hematopoietic lineage restricted progenitor cell1.03e-17120
macrophage dendritic cell progenitor5.19e-1761
hematopoietic stem cell4.48e-15168
angioblastic mesenchymal cell4.48e-15168
hematopoietic cell5.71e-15177
hematopoietic oligopotent progenitor cell2.53e-14161
hematopoietic multipotent progenitor cell2.53e-14161
myeloid cell4.03e-13108
common myeloid progenitor4.03e-13108
stuff accumulating cell1.11e-0887
granulocyte5.25e-088
Uber Anatomy
Ontology termp-valuen
adult organism4.27e-37114
hematopoietic system3.10e-2598
blood island3.10e-2598
hemolymphoid system1.99e-22108
immune system3.81e-1493
bone marrow3.87e-1476
blood6.08e-1215
haemolymphatic fluid6.08e-1215
organism substance6.08e-1215
bone element6.23e-1282
skeletal element1.56e-0990
neural tube8.27e-0956
neural rod8.27e-0956
future spinal cord8.27e-0956
neural keel8.27e-0956
regional part of nervous system2.73e-0853
regional part of brain2.73e-0853
skeletal system1.22e-07100


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.377374
MA0017.12.76432
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.16.81928
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.12.37746
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.12.63873
MA0103.11.52002
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.10.560723
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.14.49708
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
MA0137.22.70092
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#1066435.360256373075030.0064925092527670.0279559337806528
EP300#203336.77394172622320.003216880500103790.0167531556073771
RAD21#5885310.35503389545630.0009004912073565420.0066426332253927
SIN3A#2594235.408884726815140.006318961977991520.0276962426565157
SMC3#9126315.04493284493280.0002935825420371870.0030918087231846
STAT3#6774310.51946499715420.0008589184530415310.0064281321617488
TCF7L2#6934310.77017656313730.0008003181298398380.00614139788114202
ZNF143#7702313.50087655222790.0004062804962997170.00389244369810532



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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