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{{Coexpression_clusters
{
|full_id=C2564_optic_CD14_spinal_corpus_thalamus_substantia_locus
 

Latest revision as of 12:08, 17 September 2013


Full id: C2564_optic_CD14_spinal_corpus_thalamus_substantia_locus



Phase1 CAGE Peaks

Hg19::chr1:212732307..212732355,-p1@uc001hje.2
Hg19::chr4:56261764..56261833,+p3@TMEM165
Hg19::chr6:161695042..161695064,-p2@AGPAT4
Hg19::chr6:161695074..161695112,-p1@AGPAT4


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:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0103591865847246
GO:0016411acylglycerol O-acyltransferase activity0.0103591865847246
GO:0008374O-acyltransferase activity0.0151029214517312
GO:0008654phospholipid biosynthetic process0.0292229120021243
GO:0046467membrane lipid biosynthetic process0.0292229120021243
GO:0006644phospholipid metabolic process0.0381709954969072
GO:0008415acyltransferase activity0.0381709954969072
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.0381709954969072
GO:0006643membrane lipid metabolic process0.0381709954969072
GO:0016746transferase activity, transferring acyl groups0.0381709954969072
GO:0008610lipid biosynthetic process0.0390171657311839



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
defensive cell1.50e-2648
phagocyte1.50e-2648
granulocyte monocyte progenitor cell3.23e-2667
macrophage dendritic cell progenitor4.93e-2661
classical monocyte1.44e-2542
CD14-positive, CD16-negative classical monocyte1.44e-2542
monopoietic cell2.53e-2559
monocyte2.53e-2559
monoblast2.53e-2559
promonocyte2.53e-2559
myeloid lineage restricted progenitor cell3.18e-2566
myeloid leukocyte6.18e-2472
hematopoietic lineage restricted progenitor cell3.01e-20120
nongranular leukocyte1.62e-19115
leukocyte9.16e-19136
myeloid cell3.97e-14108
common myeloid progenitor3.97e-14108
hematopoietic cell7.87e-14177
hematopoietic stem cell3.00e-13168
angioblastic mesenchymal cell3.00e-13168
hematopoietic oligopotent progenitor cell6.67e-13161
hematopoietic multipotent progenitor cell6.67e-13161
stuff accumulating cell5.99e-1087
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.52e-2798
blood island1.52e-2798
neural tube1.70e-2656
neural rod1.70e-2656
future spinal cord1.70e-2656
neural keel1.70e-2656
central nervous system5.47e-2681
hemolymphoid system6.67e-26108
bone marrow1.68e-2576
regional part of nervous system9.82e-2553
regional part of brain9.82e-2553
nervous system9.98e-2489
bone element1.49e-2382
immune system1.56e-2293
brain1.88e-2168
future brain1.88e-2168
skeletal element6.21e-2090
regional part of forebrain8.12e-2041
forebrain8.12e-2041
anterior neural tube8.12e-2041
future forebrain8.12e-2041
neural plate3.73e-1982
presumptive neural plate3.73e-1982
skeletal system3.88e-19100
neurectoderm6.04e-1986
brain grey matter3.49e-1834
gray matter3.49e-1834
telencephalon4.15e-1834
regional part of telencephalon5.40e-1732
cerebral hemisphere7.21e-1732
adult organism6.64e-15114
pre-chordal neural plate8.39e-1461
cerebral cortex3.42e-1325
pallium3.42e-1325
regional part of cerebral cortex6.98e-1322
neocortex6.22e-1220
ecto-epithelium3.24e-10104
structure with developmental contribution from neural crest8.74e-10132
posterior neural tube7.54e-0815
chordal neural plate7.54e-0815
musculoskeletal system1.68e-07167
ectoderm-derived structure5.82e-07171
ectoderm5.82e-07171
presumptive ectoderm5.82e-07171
segmental subdivision of nervous system7.88e-0713


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
MA0014.10.524262
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
MA0050.11.66718
MA0051.11.91805
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
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
MA0073.10.0343867
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
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.12.78257
MA0119.10.586221
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
MA0144.11.09982
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.23.34398
MA0099.21.85039
MA0079.20.0270533
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
BATF#10538318.26835134422770.0002681660105721290.00286721846623081
E2F6#187645.017155731697390.00157802193473060.00997319412050402
EP300#203335.08045629466740.01144298405398240.0418978338106109
FOS#235348.99795530889440.0001525147711168630.00194987026327262
GATA2#262439.55869880016550.001818151618357440.0109010813978778
GTF2B#2959323.95787245074320.0001197754562855920.00162457517909233
IRF1#365935.727872815172930.008097114790333330.0320105447644645
JUN#372539.384621894252250.001918994502030470.0112860607499471
JUNB#3726322.95797449486590.0001359772504018780.00177916913739937
JUND#372735.245997956403270.01043432751748420.0386957862225173
RXRA#6256210.03730856956660.01391703805920110.0488811682483573
STAT3#677437.889598747865680.003190760481680130.0167423550013159
TBP#690843.706770687096390.005296377814784350.0244420663072009
USF1#739134.771124457905970.01370465887188020.0483074308252149
USF2#739239.74414803880220.001718341848410070.010721184318424



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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