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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:13, 17 September 2013


Full id: C2798_seminal_ductus_hippocampus_putamen_parietal_amygdala_caudate



Phase1 CAGE Peaks

Hg19::chr4:95917409..95917421,+p11@BMPR1B
Hg19::chr5:131317011..131317016,-p@chr5:131317011..131317016
-
Hg19::chr5:131335358..131335378,-p3@ACSL6
Hg19::chr5:131335380..131335396,-p4@ACSL6


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:0001550ovarian cumulus expansion0.00532783868959813
GO:0048165fused antrum stage, oogenesis0.00532783868959813
GO:0001547antral ovarian follicle growth0.00532783868959813
GO:0022605oogenesis stage0.00532783868959813
GO:0000287magnesium ion binding0.00625347626226086
GO:0005025transforming growth factor beta receptor activity, type I0.0106550500303272
GO:0015645fatty-acid ligase activity0.0112798249239386
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0112798249239386
GO:0001502cartilage condensation0.0112798249239386
GO:0046332SMAD binding0.0112798249239386
GO:0006637acyl-CoA metabolic process0.0112798249239386
GO:0048477oogenesis0.0112798249239386
GO:0007405neuroblast proliferation0.0112798249239386
GO:0030509BMP signaling pathway0.0112798249239386
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.0112798249239386
GO:0005024transforming growth factor beta receptor activity0.0112798249239386
GO:0001541ovarian follicle development0.0112798249239386
GO:0022601menstrual cycle phase0.0118754373208547
GO:0022602menstrual cycle process0.0118754373208547
GO:0008585female gonad development0.0118754373208547
GO:0009953dorsal/ventral pattern formation0.0118754373208547
GO:0016877ligase activity, forming carbon-sulfur bonds0.0118754373208547
GO:0046545development of primary female sexual characteristics0.0118754373208547
GO:0046660female sex differentiation0.0118754373208547
GO:0042698menstrual cycle0.0118754373208547
GO:0043010camera-type eye development0.0118754373208547
GO:0007292female gamete generation0.0118754373208547
GO:0051216cartilage development0.0118754373208547
GO:0060173limb development0.0118754373208547
GO:0035107appendage morphogenesis0.0118754373208547
GO:0035108limb morphogenesis0.0118754373208547
GO:0048589developmental growth0.0118754373208547
GO:0048736appendage development0.0118754373208547
GO:0048731system development0.0118754373208547
GO:0031903microbody membrane0.0122269174325372
GO:0005778peroxisomal membrane0.0122269174325372
GO:0044439peroxisomal part0.0122269174325372
GO:0044438microbody part0.0122269174325372
GO:0045597positive regulation of cell differentiation0.0122269174325372
GO:0001654eye development0.0122269174325372
GO:0048869cellular developmental process0.0122269174325372
GO:0030154cell differentiation0.0122269174325372
GO:0008406gonad development0.0125838056125745
GO:0048608reproductive structure development0.0125838056125745
GO:0048856anatomical structure development0.0135298304788747
GO:0045137development of primary sexual characteristics0.0135298304788747
GO:0048609reproductive process in a multicellular organism0.0135298304788747
GO:0032504multicellular organism reproduction0.0135298304788747
GO:0051094positive regulation of developmental process0.0147731056398816
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0159343656977792
GO:0004702receptor signaling protein serine/threonine kinase activity0.0159343656977792
GO:0007275multicellular organismal development0.0159343656977792
GO:0007548sex differentiation0.0161617906101618
GO:0005741mitochondrial outer membrane0.0161617906101618
GO:0007423sensory organ development0.0162435810661104
GO:0003002regionalization0.0162435810661104
GO:0003006reproductive developmental process0.0162435810661104
GO:0031968organelle outer membrane0.0170629428085416
GO:0019867outer membrane0.0173140632093917
GO:0042579microbody0.0174431267736113
GO:0005777peroxisome0.0174431267736113
GO:0043235receptor complex0.0188751820253275
GO:0007389pattern specification process0.0209354184380529
GO:0019199transmembrane receptor protein kinase activity0.0211059568177126
GO:0045595regulation of cell differentiation0.0235570851566974
GO:0030145manganese ion binding0.0236824483250839
GO:0005792microsome0.0257037987277299
GO:0032502developmental process0.0258298488267971
GO:0042598vesicular fraction0.02603453710581
GO:0005057receptor signaling protein activity0.0268742409044643
GO:0006631fatty acid metabolic process0.0285855311650691
GO:0001501skeletal development0.0308368239405674
GO:0005886plasma membrane0.0309517442921071
GO:0032501multicellular organismal process0.0309517442921071
GO:0050793regulation of developmental process0.0334143824400436
GO:0048699generation of neurons0.0338100634234986
GO:0022008neurogenesis0.0359262911726028
GO:0007276gamete generation0.0359262911726028
GO:0032787monocarboxylic acid metabolic process0.0381186699285198
GO:0006732coenzyme metabolic process0.0381186699285198
GO:0006954inflammatory response0.0381186699285198
GO:0007167enzyme linked receptor protein signaling pathway0.0385177082049996
GO:0009888tissue development0.0385177082049996
GO:0022414reproductive process0.0385177082049996
GO:0019953sexual reproduction0.0393067648118722
GO:0051186cofactor metabolic process0.0422844170472928
GO:0016337cell-cell adhesion0.0422844170472928
GO:0031966mitochondrial membrane0.0491083704470924



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube2.15e-10356
neural rod2.15e-10356
future spinal cord2.15e-10356
neural keel2.15e-10356
regional part of nervous system4.34e-9653
regional part of brain4.34e-9653
regional part of forebrain3.02e-8041
forebrain3.02e-8041
anterior neural tube3.02e-8041
future forebrain3.02e-8041
central nervous system1.18e-7981
brain2.53e-7868
future brain2.53e-7868
adult organism3.94e-74114
nervous system1.84e-7089
neural plate1.04e-6982
presumptive neural plate1.04e-6982
brain grey matter1.89e-6834
gray matter1.89e-6834
telencephalon2.83e-6834
neurectoderm7.14e-6686
cerebral hemisphere1.15e-6332
regional part of telencephalon1.88e-6332
pre-chordal neural plate8.56e-5461
regional part of cerebral cortex1.07e-5222
ecto-epithelium3.15e-52104
neocortex2.57e-4720
cerebral cortex7.45e-4625
pallium7.45e-4625
structure with developmental contribution from neural crest3.96e-42132
ectoderm-derived structure4.98e-32171
ectoderm4.98e-32171
presumptive ectoderm4.98e-32171
organ system subdivision8.42e-32223
tube5.81e-27192
basal ganglion1.61e-249
nuclear complex of neuraxis1.61e-249
aggregate regional part of brain1.61e-249
collection of basal ganglia1.61e-249
cerebral subcortex1.61e-249
neural nucleus4.87e-249
nucleus of brain4.87e-249
anatomical conduit3.52e-23240
posterior neural tube4.83e-2315
chordal neural plate4.83e-2315
telencephalic nucleus3.56e-197
segmental subdivision of hindbrain1.50e-1612
hindbrain1.50e-1612
presumptive hindbrain1.50e-1612
anatomical cluster2.87e-16373
gyrus4.49e-166
brainstem5.54e-166
segmental subdivision of nervous system3.92e-1513
limbic system6.00e-155
parietal lobe6.93e-145
temporal lobe7.04e-146
epithelium2.47e-13306
occipital lobe4.02e-135
cell layer4.50e-13309
diencephalon5.63e-137
future diencephalon5.63e-137
multi-tissue structure1.77e-12342
corpus striatum3.48e-124
striatum3.48e-124
ventral part of telencephalon3.48e-124
future corpus striatum3.48e-124
regional part of diencephalon8.41e-114
regional part of metencephalon4.10e-109
metencephalon4.10e-109
future metencephalon4.10e-109
organ part4.61e-10218
caudate-putamen1.32e-093
dorsal striatum1.32e-093
frontal cortex5.77e-093
medulla oblongata7.54e-093
myelencephalon7.54e-093
future myelencephalon7.54e-093
pons7.95e-093
spinal cord1.57e-083
dorsal region element1.57e-083
dorsum1.57e-083
organ5.16e-08503
germ layer1.19e-07560
germ layer / neural crest1.19e-07560
embryonic tissue1.19e-07560
presumptive structure1.19e-07560
germ layer / neural crest derived structure1.19e-07560
epiblast (generic)1.19e-07560
embryonic structure1.75e-07564
amygdala4.89e-072
Ammon's horn5.33e-072
lobe parts of cerebral cortex5.33e-072
hippocampal formation5.33e-072
limbic lobe5.33e-072
caudate nucleus7.06e-072
future caudate nucleus7.06e-072
developing anatomical structure8.61e-07581


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0055.10.125954
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
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
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
MA0111.11.57689
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
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
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

No analysis results for this cluster

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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