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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213,

Latest revision as of 11:25, 17 September 2013


Full id: C531_Neutrophils_Eosinophils_large_CD14_rectal_epitheloid_Hep2



Phase1 CAGE Peaks

Hg19::chr11:3818756..3818793,-p1@NUP98
Hg19::chr1:207495013..207495037,+p1@CD55
Hg19::chr1:207495772..207495786,+p7@CD55
Hg19::chr1:207495790..207495803,+p17@CD55
Hg19::chr1:207495844..207495859,+p14@CD55
Hg19::chr1:207497905..207497939,+p3@CD55
Hg19::chr1:207497946..207497958,+p11@CD55
Hg19::chr1:207497988..207498028,+p4@CD55
Hg19::chr1:207498974..207498994,+p9@CD55
Hg19::chr1:207498999..207499011,+p13@CD55
Hg19::chr1:207499012..207499044,+p5@CD55
Hg19::chr1:207500090..207500105,+p6@CD55
Hg19::chr1:207504446..207504457,+p@chr1:207504446..207504457
+
Hg19::chr1:207504490..207504510,+p@chr1:207504490..207504510
+
Hg19::chr1:207504564..207504579,+p@chr1:207504564..207504579
+
Hg19::chr1:207504605..207504622,+p@chr1:207504605..207504622
+
Hg19::chr1:207510129..207510165,-p@chr1:207510129..207510165
-


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:0006999nuclear pore organization and biogenesis0.0122744532210089
GO:0045730respiratory burst0.0122744532210089
GO:0017056structural constituent of nuclear pore0.0190924697548727
GO:0000059protein import into nucleus, docking0.0218419002159206
GO:0006958complement activation, classical pathway0.0218419002159206
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0218419002159206
GO:0006997nuclear organization and biogenesis0.0218419002159206
GO:0006956complement activation0.0218419002159206
GO:0002541activation of plasma proteins during acute inflammatory response0.0218419002159206
GO:0045121lipid raft0.0218419002159206
GO:0016064immunoglobulin mediated immune response0.0218419002159206
GO:0019724B cell mediated immunity0.0218419002159206
GO:0043623cellular protein complex assembly0.0218419002159206
GO:0065002intracellular protein transport across a membrane0.0218419002159206
GO:0051480cytosolic calcium ion homeostasis0.0218419002159206
GO:0007204elevation of cytosolic calcium ion concentration0.0218419002159206
GO:0002253activation of immune response0.0218419002159206
GO:0002449lymphocyte mediated immunity0.0218419002159206
GO:0006959humoral immune response0.0218419002159206
GO:0002250adaptive immune response0.0218419002159206
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0218419002159206
GO:0002443leukocyte mediated immunity0.0218419002159206
GO:0002526acute inflammatory response0.0218419002159206
GO:0051028mRNA transport0.0218419002159206
GO:0050778positive regulation of immune response0.0218419002159206
GO:0002684positive regulation of immune system process0.0218419002159206
GO:0005643nuclear pore0.0218419002159206
GO:0050658RNA transport0.0218419002159206
GO:0051236establishment of RNA localization0.0218419002159206
GO:0050657nucleic acid transport0.0218419002159206
GO:0006403RNA localization0.0218419002159206
GO:0006606protein import into nucleus0.0218419002159206
GO:0046930pore complex0.0218419002159206
GO:0050776regulation of immune response0.0218419002159206
GO:0051170nuclear import0.0218419002159206
GO:0002682regulation of immune system process0.0218419002159206
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0218419002159206
GO:0051240positive regulation of multicellular organismal process0.0218419002159206
GO:0002252immune effector process0.0218419002159206
GO:0044453nuclear membrane part0.0218419002159206
GO:0045087innate immune response0.0218419002159206
GO:0006874cellular calcium ion homeostasis0.0218419002159206
GO:0055074calcium ion homeostasis0.0218419002159206
GO:0017038protein import0.0218419002159206
GO:0006875cellular metal ion homeostasis0.0218419002159206
GO:0055065metal ion homeostasis0.0218419002159206
GO:0048503GPI anchor binding0.0218976048652095
GO:0031965nuclear membrane0.02547336752759
GO:0006913nucleocytoplasmic transport0.02547336752759
GO:0051169nuclear transport0.02547336752759
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0287214589601625
GO:0055066di-, tri-valent inorganic cation homeostasis0.0287214589601625
GO:0005635nuclear envelope0.0298685474727805
GO:0030003cellular cation homeostasis0.0301136843778026
GO:0055080cation homeostasis0.0301136843778026
GO:0006605protein targeting0.0317543212284013
GO:0005625soluble fraction0.0327573563177623
GO:0055082cellular chemical homeostasis0.0327573563177623
GO:0006873cellular ion homeostasis0.0327573563177623
GO:0035091phosphoinositide binding0.0341071295173144
GO:0050801ion homeostasis0.0356780789030172
GO:0051239regulation of multicellular organismal process0.0364119499824043
GO:0006954inflammatory response0.0376372976168732
GO:0048878chemical homeostasis0.0384434488269865
GO:0005543phospholipid binding0.041843015573562
GO:0006461protein complex assembly0.0419455896578316
GO:0006260DNA replication0.0431328841847652
GO:0019725cellular homeostasis0.0448795788258851
GO:0009893positive regulation of metabolic process0.0461053402929223
GO:0009611response to wounding0.0491428245464635



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
classical monocyte5.30e-2442
CD14-positive, CD16-negative classical monocyte5.30e-2442
defensive cell5.79e-2048
phagocyte5.79e-2048
myeloid leukocyte3.74e-1872
granulocyte monocyte progenitor cell1.33e-1567
leukocyte1.69e-15136
myeloid lineage restricted progenitor cell1.78e-1566
myeloid cell2.84e-15108
common myeloid progenitor2.84e-15108
macrophage dendritic cell progenitor5.64e-1561
monopoietic cell6.60e-1459
monocyte6.60e-1459
monoblast6.60e-1459
promonocyte6.60e-1459
hematopoietic stem cell3.04e-13168
angioblastic mesenchymal cell3.04e-13168
hematopoietic oligopotent progenitor cell3.06e-13161
hematopoietic multipotent progenitor cell3.06e-13161
hematopoietic lineage restricted progenitor cell7.77e-13120
hematopoietic cell1.03e-11177
nongranular leukocyte3.16e-11115
stuff accumulating cell1.52e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.30e-1498
blood island7.30e-1498
hemolymphoid system1.12e-12108
bone marrow2.67e-1176
bone element5.72e-1182
immune system1.13e-0993
skeletal element1.56e-0890
larynx5.35e-089
skeletal system1.12e-07100


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)
MA0003.10.000498485
MA0004.10.221943
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.00118158
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.608306
MA0043.10.621991
MA0046.11.48543
MA0048.10.0140676
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.00123747
MA0056.10
MA0057.10.0616251
MA0058.10.153757
MA0059.10.15289
MA0060.10.0509127
MA0061.10.0397345
MA0063.10
MA0066.12.26462
MA0067.10.924196
MA0068.10.0264141
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.000460837
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.12.6496
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.00460154
MA0089.10
MA0090.10.174619
MA0091.10.636604
MA0092.10.195947
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.34743
MA0105.10.0103933
MA0106.10.33677
MA0107.10.0748038
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.924932
MA0114.10.072201
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.11.73305
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.12.64878
MA0136.10.30842
MA0139.10.0351037
MA0140.10.269307
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.10.00588885
MA0146.17.9117e-05
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.00269755
MA0138.20.38342
MA0002.20.393994
MA0137.20.398112
MA0104.20.188874
MA0047.20.326636
MA0112.21.0853
MA0065.20.00623543
MA0150.10.170499
MA0151.10
MA0152.10.753898
MA0153.11.69994
MA0154.10.00994595
MA0155.10.0782503
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.10.703717
MA0161.10
MA0162.10.00317087
MA0163.10.000152387
MA0164.10.361105
MA0080.20.11444
MA0018.20.337929
MA0099.20.27482
MA0079.25.83152e-08
MA0102.21.14323
MA0258.10.82387
MA0259.10.0828875
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
POLR2A#5430172.147453176558072.27473247069268e-068.12763546037197e-05



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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