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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:29, 17 September 2013


Full id: C701_Mast_thalamus_globus_middle_substantia_corpus_medial



Phase1 CAGE Peaks

Hg19::chr15:42696918..42696927,+p9@CAPN3
Hg19::chr6:134638696..134638707,-p25@SGK1
Hg19::chr6:134639042..134639056,-p14@SGK1
Hg19::chr6:134639058..134639085,-p10@SGK1
Hg19::chr6:134639090..134639119,-p6@SGK1
Hg19::chr6:134639126..134639137,-p32@SGK1
Hg19::chr6:134639140..134639171,-p7@SGK1
Hg19::chr6:134639180..134639220,-p4@SGK1
Hg19::chr6:134639235..134639255,-p8@SGK1
Hg19::chr7:104909435..104909535,-p2@SRPK2
Hg19::chr7:117513474..117513500,-p1@CTTNBP2
Hg19::chr7:117513540..117513587,-p2@CTTNBP2


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:0031116positive regulation of microtubule polymerization0.0186801036130093
GO:0050998nitric-oxide synthase binding0.0186801036130093
GO:0031112positive regulation of microtubule polymerization or depolymerization0.0186801036130093
GO:0030321transepithelial chloride transport0.0186801036130093
GO:0031113regulation of microtubule polymerization0.0186801036130093
GO:0046785microtubule polymerization0.0186801036130093
GO:0032502developmental process0.0186801036130093
GO:0001937negative regulation of endothelial cell proliferation0.0186801036130093
GO:0051130positive regulation of cellular component organization and biogenesis0.0186801036130093
GO:0045178basal part of cell0.0186801036130093
GO:0009925basal plasma membrane0.0186801036130093
GO:0001936regulation of endothelial cell proliferation0.0186801036130093
GO:0019905syntaxin binding0.0186801036130093
GO:0042311vasodilation0.0186801036130093
GO:0001935endothelial cell proliferation0.0186801036130093
GO:0030317sperm motility0.0186801036130093
GO:0000149SNARE binding0.0186801036130093
GO:0007595lactation0.0186801036130093
GO:0043434response to peptide hormone stimulus0.0186801036130093
GO:0043627response to estrogen stimulus0.0186801036130093
GO:0016599caveolar membrane0.0186801036130093
GO:0005901caveola0.0186801036130093
GO:0031110regulation of microtubule polymerization or depolymerization0.0186801036130093
GO:0004198calcium-dependent cysteine-type endopeptidase activity0.0186801036130093
GO:0000245spliceosome assembly0.0186801036130093
GO:0031109microtubule polymerization or depolymerization0.0186801036130093
GO:0019861flagellum0.0186801036130093
GO:0005925focal adhesion0.0186801036130093
GO:0001764neuron migration0.0186801036130093
GO:0048545response to steroid hormone stimulus0.0186801036130093
GO:0048513organ development0.0186801036130093
GO:0005924cell-substrate adherens junction0.0186801036130093
GO:0004672protein kinase activity0.0186801036130093
GO:0006468protein amino acid phosphorylation0.0186801036130093
GO:0030055cell-matrix junction0.0186801036130093
GO:0030324lung development0.0186801036130093
GO:0035150regulation of tube size0.0186801036130093
GO:0050880regulation of blood vessel size0.0186801036130093
GO:0030323respiratory tube development0.0186801036130093
GO:0003018vascular process in circulatory system0.0186801036130093
GO:0046777protein amino acid autophosphorylation0.0186801036130093
GO:0045121lipid raft0.0186801036130093
GO:0016540protein autoprocessing0.0186801036130093
GO:0044267cellular protein metabolic process0.019975165662148
GO:0044260cellular macromolecule metabolic process0.0202967030143573
GO:0005912adherens junction0.02039706182063
GO:0016310phosphorylation0.02039706182063
GO:0016773phosphotransferase activity, alcohol group as acceptor0.02039706182063
GO:0019538protein metabolic process0.0207095077449335
GO:0048609reproductive process in a multicellular organism0.0208765004351701
GO:0032504multicellular organism reproduction0.0208765004351701
GO:0042493response to drug0.0211450960231025
GO:0016324apical plasma membrane0.0218118710033986
GO:0000398nuclear mRNA splicing, via spliceosome0.0218118710033986
GO:0000375RNA splicing, via transesterification reactions0.0218118710033986
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0218118710033986
GO:0048731system development0.0225153910667357
GO:0009725response to hormone stimulus0.0228608169243905
GO:0016301kinase activity0.0233437865526716
GO:0006793phosphorus metabolic process0.0233437865526716
GO:0006796phosphate metabolic process0.0233437865526716
GO:0035239tube morphogenesis0.0233437865526716
GO:0016323basolateral plasma membrane0.0233437865526716
GO:0045177apical part of cell0.0233437865526716
GO:0006821chloride transport0.0233437865526716
GO:0048869cellular developmental process0.0242610472914439
GO:0030154cell differentiation0.0242610472914439
GO:0051258protein polymerization0.0245550436696403
GO:0019900kinase binding0.0245550436696403
GO:0016485protein processing0.0245550436696403
GO:0051128regulation of cellular component organization and biogenesis0.0245550436696403
GO:0000226microtubule cytoskeleton organization and biogenesis0.0246968259458888
GO:0030659cytoplasmic vesicle membrane0.0250727235879941
GO:0044433cytoplasmic vesicle part0.0252035395469867
GO:0016772transferase activity, transferring phosphorus-containing groups0.0253631517374223
GO:0012506vesicle membrane0.0258025127592807
GO:0048856anatomical structure development0.0258025127592807
GO:0035295tube development0.0261380241335892
GO:0005737cytoplasm0.0267665293047419
GO:0007420brain development0.0297900844702313
GO:0022618protein-RNA complex assembly0.0297900844702313
GO:0043687post-translational protein modification0.0297900844702313
GO:0004197cysteine-type endopeptidase activity0.0297900844702313
GO:0007275multicellular organismal development0.0309125018910617
GO:0008015blood circulation0.0323781891794638
GO:0003013circulatory system process0.0323781891794638
GO:0007517muscle development0.0343943065693929
GO:0006464protein modification process0.0404822434922459
GO:0043412biopolymer modification0.0429476695999892
GO:0008285negative regulation of cell proliferation0.0429476695999892
GO:0008380RNA splicing0.0429476695999892
GO:0016477cell migration0.0434120560477655
GO:0005625soluble fraction0.0434120560477655
GO:0007417central nervous system development0.0434120560477655
GO:0048699generation of neurons0.0442254649823763
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0444829172976253
GO:0015698inorganic anion transport0.0463873480793026
GO:0022008neurogenesis0.0463873480793026
GO:0006397mRNA processing0.0478311459301994



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
histamine secreting cell7.56e-095
biogenic amine secreting cell7.56e-095
granulocytopoietic cell7.56e-095
mast cell7.56e-095
mast cell progenitor7.56e-095
basophil mast progenitor cell7.56e-095
endocrine cell7.27e-089
melanocyte3.03e-0710
melanoblast3.03e-0710
Uber Anatomy
Ontology termp-valuen
neural tube5.70e-5756
neural rod5.70e-5756
future spinal cord5.70e-5756
neural keel5.70e-5756
central nervous system3.58e-5581
nervous system2.07e-5389
adult organism2.68e-53114
regional part of nervous system5.03e-5353
regional part of brain5.03e-5353
brain7.24e-4768
future brain7.24e-4768
regional part of forebrain1.05e-4441
forebrain1.05e-4441
anterior neural tube1.05e-4441
future forebrain1.05e-4441
brain grey matter5.82e-4134
gray matter5.82e-4134
telencephalon6.48e-4134
neural plate5.30e-4082
presumptive neural plate5.30e-4082
neurectoderm1.08e-3886
regional part of telencephalon3.89e-3832
cerebral hemisphere6.47e-3832
pre-chordal neural plate5.73e-3161
structure with developmental contribution from neural crest4.03e-30132
ecto-epithelium7.73e-29104
regional part of cerebral cortex1.61e-2822
cerebral cortex2.21e-2825
pallium2.21e-2825
ectoderm-derived structure6.96e-28171
ectoderm6.96e-28171
presumptive ectoderm6.96e-28171
neocortex1.10e-2520
organ system subdivision3.24e-22223
neural nucleus4.90e-149
nucleus of brain4.90e-149
basal ganglion7.86e-149
nuclear complex of neuraxis7.86e-149
aggregate regional part of brain7.86e-149
collection of basal ganglia7.86e-149
cerebral subcortex7.86e-149
posterior neural tube4.57e-1315
chordal neural plate4.57e-1315
telencephalic nucleus2.75e-117
segmental subdivision of nervous system6.75e-1113
anatomical cluster8.07e-11373
tube2.10e-10192
organ6.39e-10503
embryo6.80e-10592
brainstem9.40e-106
segmental subdivision of hindbrain1.51e-0912
hindbrain1.51e-0912
presumptive hindbrain1.51e-0912
gyrus2.76e-096
developing anatomical structure6.58e-09581
embryonic structure7.58e-09564
germ layer1.09e-08560
germ layer / neural crest1.09e-08560
embryonic tissue1.09e-08560
presumptive structure1.09e-08560
germ layer / neural crest derived structure1.09e-08560
epiblast (generic)1.09e-08560
limbic system2.44e-085
occipital lobe3.73e-085
parietal lobe5.51e-085
temporal lobe6.33e-086
anatomical conduit9.55e-08240
multi-cellular organism2.80e-07656
corpus striatum5.44e-074
striatum5.44e-074
ventral part of telencephalon5.44e-074
future corpus striatum5.44e-074
organ part6.10e-07218
regional part of diencephalon8.22e-074


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)
MA0003.11.34964
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.657865
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.583404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.11.87299
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.4241
MA0050.10.311321
MA0051.10.410316
MA0052.13.99404
MA0055.10.107116
MA0056.10
MA0057.10.0373953
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.10.0856761
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.11.83363e-05
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0178242
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.181541
MA0105.10.0320473
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.0781324
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.0212759
MA0146.10.000996775
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.280813
MA0035.20.376007
MA0039.20.0117227
MA0138.20.503176
MA0002.20.0954816
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.20.0192555
MA0065.20.0221687
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.13.33201
MA0155.10.0793743
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.10.138499
MA0163.10.0909552
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.20.0178219
MA0102.21.28978
MA0258.10.754226
MA0259.10.149181
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#10664104.466880310895862.32271458385553e-068.25389548905367e-05
RAD21#588597.766275421592251.22173700731638e-077.02626604114072e-06



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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