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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:21, 17 September 2013


Full id: C368_Pericytes_Fibroblast_Nucleus_Anulus_Meningeal_Mesenchymal_Smooth



Phase1 CAGE Peaks

Hg19::chr11:130318529..130318547,+p1@ADAMTS15
Hg19::chr11:60610073..60610090,+p6@CCDC86
Hg19::chr11:61634723..61634731,+p@chr11:61634723..61634731
+
Hg19::chr11:61634768..61634777,+p@chr11:61634768..61634777
+
Hg19::chr12:279773..279812,+p@chr12:279773..279812
+
Hg19::chr12:279860..279871,+p@chr12:279860..279871
+
Hg19::chr12:57522813..57522825,-p10@STAT6
Hg19::chr15:57598803..57598812,+p6@LOC283663
Hg19::chr17:48346424..48346435,+p@chr17:48346424..48346435
+
Hg19::chr17:75446704..75446713,+p35@SEPT9
Hg19::chr17:75446731..75446743,+p36@SEPT9
Hg19::chr17:75446774..75446783,+p49@SEPT9
Hg19::chr17:75446796..75446809,+p23@SEPT9
Hg19::chr17:75446824..75446838,+p9@SEPT9
Hg19::chr17:75447512..75447527,+p22@SEPT9
Hg19::chr17:75471711..75471726,+p73@SEPT9
Hg19::chr1:19778678..19778689,-p@chr1:19778678..19778689
-
Hg19::chr1:19778700..19778738,-p@chr1:19778700..19778738
-
Hg19::chr3:147109858..147109861,+p@chr3:147109858..147109861
+
Hg19::chr3:147112699..147112713,-p@chr3:147112699..147112713
-
Hg19::chr3:147127904..147127942,+p1@AB464362
Hg19::chr3:147127961..147127972,+p3@AB464362
Hg19::chr3:147128031..147128038,+p7@AB464362
Hg19::chr3:147128048..147128057,+p4@AB464362
Hg19::chr5:149515832..149515837,-p@chr5:149515832..149515837
-
Hg19::chr5:149532703..149532711,+p@chr5:149532703..149532711
+
Hg19::chr5:149537789..149537803,-p@chr5:149537789..149537803
-
Hg19::chr5:149537807..149537827,-p@chr5:149537807..149537827
-
Hg19::chr5:72744336..72744359,-p5@FOXD1
Hg19::chr9:139876143..139876170,+p1@LCNL1


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:0048295positive regulation of isotype switching to IgE isotypes0.0131869235943323
GO:0048289isotype switching to IgE isotypes0.0131869235943323
GO:0002829negative regulation of T-helper 2 type immune response0.0131869235943323
GO:0002828regulation of T-helper 2 type immune response0.0131869235943323
GO:0048293regulation of isotype switching to IgE isotypes0.0131869235943323
GO:0002820negative regulation of adaptive immune response0.0131869235943323
GO:0002823negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0131869235943323
GO:0045830positive regulation of isotype switching0.0131869235943323
GO:0051291protein heterooligomerization0.0131869235943323
GO:0050777negative regulation of immune response0.0131869235943323
GO:0045191regulation of isotype switching0.0131869235943323
GO:0002683negative regulation of immune system process0.0131869235943323
GO:0042092T-helper 2 type immune response0.0131869235943323
GO:0002208somatic diversification of immunoglobulins during immune response0.0131869235943323
GO:0002381immunoglobulin production during immune response0.0131869235943323
GO:0002204somatic recombination of immunoglobulin genes during immune response0.0131869235943323
GO:0008301DNA bending activity0.0131869235943323
GO:0032432actin filament bundle0.0131869235943323
GO:0045190isotype switching0.0131869235943323
GO:0001725stress fiber0.0131869235943323
GO:0016447somatic recombination of immunoglobulin gene segments0.0135501835469304
GO:0002819regulation of adaptive immune response0.0135501835469304
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.0135501835469304
GO:0016444somatic cell DNA recombination0.0138291801550393
GO:0016445somatic diversification of immunoglobulins0.0138291801550393
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0138291801550393
GO:0002200somatic diversification of immune receptors0.0142039512283195
GO:0002377immunoglobulin production0.0148756627066806
GO:0050871positive regulation of B cell activation0.0148756627066806
GO:0051241negative regulation of multicellular organismal process0.0193197341117233
GO:0050864regulation of B cell activation0.0193197341117233
GO:0002440production of molecular mediator of immune response0.0202108918231167
GO:0043565sequence-specific DNA binding0.0308738063090595
GO:0051251positive regulation of lymphocyte activation0.0345488266684464
GO:0016064immunoglobulin mediated immune response0.0345488266684464
GO:0019724B cell mediated immunity0.0345488266684464
GO:0042113B cell activation0.0390018187822978
GO:0051259protein oligomerization0.0390018187822978
GO:0048471perinuclear region of cytoplasm0.0392230169527433
GO:0002449lymphocyte mediated immunity0.0413951774132484
GO:0002250adaptive immune response0.0413951774132484
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0413951774132484
GO:0051249regulation of lymphocyte activation0.0413951774132484
GO:0048519negative regulation of biological process0.0413951774132484
GO:0002443leukocyte mediated immunity0.0413951774132484
GO:0050865regulation of cell activation0.0415287325000021
GO:0050776regulation of immune response0.0496894167890069
GO:0002682regulation of immune system process0.0496894167890069



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>

Uber Anatomy
Ontology termp-valuen
vasculature of organ4.47e-2511
brain8.27e-2268
future brain8.27e-2268
central nervous system5.16e-2081
brain vasculature3.03e-195
blood-cerebrospinal fluid barrier2.59e-183
ciliary epithelium1.15e-173
ciliary body1.15e-173
nervous system1.18e-1789
neural plate1.71e-1582
presumptive neural plate1.71e-1582
neurectoderm1.29e-1486
regional part of nervous system1.61e-1453
regional part of brain1.61e-1453
neural tube1.28e-1356
neural rod1.28e-1356
future spinal cord1.28e-1356
neural keel1.28e-1356
atypical epithelium2.19e-134
ectoderm-derived structure2.76e-13171
ectoderm2.76e-13171
presumptive ectoderm2.76e-13171
vascular plexus5.24e-132
ventricle of nervous system5.24e-132
choroid plexus5.24e-132
brain ventricle5.24e-132
ventricular system of brain5.24e-132
ventricular system of central nervous system5.24e-132
segmental subdivision of hindbrain1.34e-1112
hindbrain1.34e-1112
presumptive hindbrain1.34e-1112
ecto-epithelium1.68e-11104
intervertebral cartilage5.54e-115
symphysis5.54e-115
nonsynovial joint5.54e-115
fibrous joint5.54e-115
cartilaginous joint5.54e-115
developing mesenchymal condensation5.54e-115
pre-cartilage condensation5.54e-115
cartilaginous condensation5.54e-115
cartilage element5.54e-115
post-cranial axial skeletal system5.54e-115
vertebral column5.54e-115
intervertebral disk5.54e-115
intervertebral joint5.54e-115
segmental subdivision of nervous system1.09e-1013
pre-chordal neural plate2.51e-1061
regional part of metencephalon2.99e-109
metencephalon2.99e-109
future metencephalon2.99e-109
structure with developmental contribution from neural crest1.53e-09132
posterior neural tube3.13e-0915
chordal neural plate3.13e-0915
cerebellum4.27e-096
rhombic lip4.27e-096
vasculature of eye4.39e-096
uvea4.39e-096
vasculature of head4.39e-096
telencephalon9.90e-0934
neocortex1.04e-0820
nucleus pulposus1.10e-083
axial mesoderm1.10e-083
notochord1.10e-083
chordamesoderm1.10e-083
regional part of cerebral cortex6.64e-0822
organ system subdivision3.27e-07223
cerebral hemisphere3.57e-0732
regional part of forebrain4.36e-0741
forebrain4.36e-0741
anterior neural tube4.36e-0741
future forebrain4.36e-0741
articulation5.03e-078
skeletal joint5.03e-078
articular system5.03e-078
cerebral cortex6.26e-0725
pallium6.26e-0725
paracentral gyrus7.15e-071
corpus callosum7.57e-071
central nervous system cell part cluster7.57e-071
axon tract7.57e-071
intercerebral commissure7.57e-071
dorsal telencephalic commissure7.57e-071
brain white matter7.57e-071
brain commissure7.57e-071
white matter7.57e-071
nervous system commissure7.57e-071
cerebral hemisphere white matter7.57e-071
postcentral gyrus8.02e-071
dura mater8.49e-071


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)
MA0003.11.24235
MA0004.10.0961566
MA0006.10.0332857
MA0007.10.612505
MA0009.10.417521
MA0014.10.0116099
MA0017.11.07347
MA0019.10.180682
MA0024.12.41036
MA0025.10.531977
MA0027.11.95983
MA0028.10.346327
MA0029.10.347825
MA0030.10.338746
MA0031.10.288912
MA0038.10.15256
MA0040.10.92917
MA0041.10.343445
MA0042.10.0896515
MA0043.10.417784
MA0046.10.408463
MA0048.10.246211
MA0050.10.0900741
MA0051.10.150026
MA0052.10.355576
MA0055.11.45189
MA0056.10
MA0057.14.53052
MA0058.10.0546193
MA0059.10.441047
MA0060.10.128077
MA0061.10.205567
MA0063.10
MA0066.10.152817
MA0067.10.697961
MA0068.10.416765
MA0069.10.405267
MA0070.10.396023
MA0071.10.407159
MA0072.10.392323
MA0073.12.78749
MA0074.10.149576
MA0076.10.477402
MA0077.11.00303
MA0078.10.213745
MA0081.10.441387
MA0083.10.423797
MA0084.10.873335
MA0087.10.390315
MA0088.11.74859
MA0089.10
MA0090.10.508642
MA0091.10.0974512
MA0092.11.99739
MA0093.10.137242
MA0095.10
MA0098.10
MA0100.10.94126
MA0101.10.140397
MA0103.10.125753
MA0105.13.73481
MA0106.10.527317
MA0107.10.0171106
MA0108.20.286605
MA0109.10
MA0111.10.538416
MA0113.10.55303
MA0114.11.28653
MA0115.10.62811
MA0116.12.73912
MA0117.11.14035
MA0119.10.407887
MA0122.10.471243
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.226279
MA0132.10
MA0133.10
MA0135.11.12711
MA0136.10.156833
MA0139.11.76143
MA0140.10.403323
MA0141.10.437416
MA0142.10.265252
MA0143.10.553308
MA0144.10.567573
MA0145.11.94091
MA0146.11.65374
MA0147.10.0184972
MA0148.10.352161
MA0149.10.389467
MA0062.20.0896156
MA0035.20.128078
MA0039.22.2851
MA0138.20.614598
MA0002.20.113455
MA0137.20.358888
MA0104.20.00891586
MA0047.20.170483
MA0112.20.995408
MA0065.20.65029
MA0150.10.853276
MA0151.10
MA0152.10.132183
MA0153.10.501603
MA0154.19.17245
MA0155.11.16903
MA0156.10.0408263
MA0157.10.245386
MA0158.10
MA0159.10.407932
MA0160.10.116872
MA0161.10
MA0162.10.582787
MA0163.12.28494
MA0164.10.196993
MA0080.20.137324
MA0018.20.179075
MA0099.22.59258
MA0079.211.7758
MA0102.20.908736
MA0258.11.13577
MA0259.10.428772
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
FOSL1#806156.618929952728830.0008510821723464740.00640944411578406
FOSL2#235563.386040120912340.007369575523568160.0304651321289556
HNF4A#317264.626458072590740.001578094417127210.00994656625409467
HNF4G#317465.750684505289360.0005102613402789160.00446698944823048
JUNB#372655.101772109970190.002675252841566160.0147487717229903
NR2C2#718255.435768484206810.002031864570411240.0118023305822681
SUZ12#2351246.682104121475050.002866208855127340.0155309736754511



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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