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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.241841199755703,-

Latest revision as of 11:36, 17 September 2013


Full id: C1055_CD19_thymus_CD4_CD8_Neutrophils_Natural_cerebellum



Phase1 CAGE Peaks

Hg19::chr17:8151353..8151381,-p1@CTC1
Hg19::chr1:204485503..204485555,+p1@MDM4
Hg19::chr2:206950781..206950947,-p1@INO80D
Hg19::chr4:76439596..76439643,-p2@RCHY1
Hg19::chr4:78741389..78741433,-p@chr4:78741389..78741433
-
Hg19::chr5:56469653..56469722,+p2@GPBP1
Hg19::chr7:21467642..21467671,+p2@SP4
Hg19::chr7:21467674..21467727,+p1@SP4


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:0045023G0 to G1 transition0.0105964942920282
GO:0000320re-entry into mitotic cell cycle0.0105964942920282
GO:0042177negative regulation of protein catabolic process0.0190677949582778
GO:0006357regulation of transcription from RNA polymerase II promoter0.0190677949582778
GO:0009895negative regulation of catabolic process0.0190677949582778
GO:0050821protein stabilization0.0233248915267865
GO:0042176regulation of protein catabolic process0.0233248915267865
GO:0006366transcription from RNA polymerase II promoter0.0233248915267865
GO:0031647regulation of protein stability0.0247044173842433
GO:0009894regulation of catabolic process0.026464343452305



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
leukocyte6.80e-40136
hematopoietic stem cell8.80e-39168
angioblastic mesenchymal cell8.80e-39168
hematopoietic oligopotent progenitor cell2.03e-35161
hematopoietic multipotent progenitor cell2.03e-35161
hematopoietic cell1.02e-34177
hematopoietic lineage restricted progenitor cell5.15e-32120
nongranular leukocyte8.18e-31115
nucleate cell3.35e-2255
lymphocyte1.34e-2153
common lymphoid progenitor1.34e-2153
lymphoid lineage restricted progenitor cell1.87e-2152
myeloid cell6.16e-15108
common myeloid progenitor6.16e-15108
myeloid leukocyte4.64e-1472
mature alpha-beta T cell6.85e-1218
alpha-beta T cell6.85e-1218
immature T cell6.85e-1218
mature T cell6.85e-1218
immature alpha-beta T cell6.85e-1218
classical monocyte1.70e-1142
CD14-positive, CD16-negative classical monocyte1.70e-1142
granulocyte monocyte progenitor cell2.14e-1167
myeloid lineage restricted progenitor cell3.44e-1166
T cell5.90e-1125
pro-T cell5.90e-1125
lymphocyte of B lineage6.67e-1024
pro-B cell6.67e-1024
macrophage dendritic cell progenitor6.94e-1061
defensive cell1.45e-0948
phagocyte1.45e-0948
monopoietic cell2.82e-0959
monocyte2.82e-0959
monoblast2.82e-0959
promonocyte2.82e-0959
B cell2.61e-0814
CD8-positive, alpha-beta T cell3.16e-0811
Uber Anatomy
Ontology termp-valuen
adult organism2.14e-30114
hematopoietic system1.29e-1598
blood island1.29e-1598
neural tube1.69e-1456
neural rod1.69e-1456
future spinal cord1.69e-1456
neural keel1.69e-1456
hemolymphoid system1.72e-14108
regional part of nervous system1.54e-1353
regional part of brain1.54e-1353
regional part of forebrain1.99e-1241
forebrain1.99e-1241
anterior neural tube1.99e-1241
future forebrain1.99e-1241
nervous system8.53e-1289
central nervous system1.03e-1181
telencephalon3.04e-1034
brain grey matter4.03e-1034
gray matter4.03e-1034
brain5.02e-1068
future brain5.02e-1068
regional part of telencephalon1.47e-0932
cerebral hemisphere1.94e-0932
immune system2.29e-0993
bone marrow4.49e-0876
blood5.53e-0815
haemolymphatic fluid5.53e-0815
organism substance5.53e-0815
neurectoderm8.78e-0886
bone element9.36e-0882
regional part of cerebral cortex9.65e-0822
neocortex2.20e-0720
cerebral cortex2.68e-0725
pallium2.68e-0725
neural plate2.68e-0782
presumptive neural plate2.68e-0782


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)
MA0003.10.797136
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.12.22106
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.11.52958
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.524515
MA0056.10
MA0057.12.14064
MA0058.10.950944
MA0059.10.361075
MA0060.11.06021
MA0061.12.9227
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.12.06698
MA0071.10.518907
MA0072.10.888148
MA0073.15.51347
MA0074.10.552456
MA0076.11.74818
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.11.49614
MA0103.10.291333
MA0105.11.47197
MA0106.10.59853
MA0107.12.69808
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.480646
MA0146.10.934908
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.21.50503
MA0035.20.515566
MA0039.23.94096
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.21.05746
MA0047.20.586412
MA0112.20.0572179
MA0065.21.27835
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.11.16939
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.93331
MA0163.12.76433
MA0164.10.627336
MA0080.20.303167
MA0018.22.48749
MA0099.20.523145
MA0079.28.5976
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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#90564.752151182721970.0003235895417103970.0033109991326239
E2F1#186974.293965563019419.58670853279727e-050.00137060404169311
E2F6#187653.135722332310870.01024880501420960.0381513739263985
EGR1#195853.117611934256340.01051390990388360.0389218147047958
HEY1#2346284.040111043105711.4081650274634e-050.000339099255944779
HMGN3#932455.111592327094120.001109515975889930.0077086707694231
IRF1#365943.818581876781950.01326136316826170.0469047516909403
NFKB1#479074.802055496169614.48248622098168e-050.00079387210180279
PAX5#507954.168478456986140.002847508706107280.0154376537456986
PBX3#5090410.95725634337210.0002614921975631970.00280159864806142
POLR2A#543082.147453176558070.002210725788971910.0127209912217321
POU2F2#545244.553062028871260.007062473846831130.0294603069892238
TAF1#687283.343046285745296.40776711117462e-050.0010435377971682
TAF7#687945.716534702461960.003068541555180160.0161766398203756
TBP#690862.780078015322290.006390181121263010.0278041963972665
YY1#752874.297274406122129.53674534900876e-050.00136458165160313
ZNF263#1012744.110920818505340.01019992782316260.0379924484440702



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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