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{{Coexpression_clusters
{
|full_id=C1279_CD14_Neutrophils_substantia_Eosinophils_optic_globus_thalamus
 

Latest revision as of 11:41, 17 September 2013


Full id: C1279_CD14_Neutrophils_substantia_Eosinophils_optic_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr6:163841233..163841239,+p@chr6:163841233..163841239
+
Hg19::chr6:163848296..163848300,+p@chr6:163848296..163848300
+
Hg19::chr6:163849791..163849795,+p20@QKI
Hg19::chr6:163910016..163910030,+p@chr6:163910016..163910030
+
Hg19::chr6:163910203..163910206,+p@chr6:163910203..163910206
+
Hg19::chr6:163924190..163924195,+p@chr6:163924190..163924195
+
Hg19::chr6:163928513..163928551,+p1@BC044915


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:0051028mRNA transport0.0280623258369638
GO:0050658RNA transport0.0280623258369638
GO:0051236establishment of RNA localization0.0280623258369638
GO:0050657nucleic acid transport0.0280623258369638
GO:0006403RNA localization0.0280623258369638
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0280623258369638
GO:0006417regulation of translation0.036427057576828
GO:0031326regulation of cellular biosynthetic process0.036427057576828
GO:0009889regulation of biosynthetic process0.036427057576828
GO:0008380RNA splicing0.036427057576828
GO:0006397mRNA processing0.0401801483574708
GO:0016071mRNA metabolic process0.0461409395973154



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
myeloid leukocyte2.55e-3272
macrophage dendritic cell progenitor2.33e-2761
granulocyte monocyte progenitor cell2.75e-2767
monopoietic cell3.37e-2659
monocyte3.37e-2659
monoblast3.37e-2659
promonocyte3.37e-2659
classical monocyte6.07e-2642
CD14-positive, CD16-negative classical monocyte6.07e-2642
myeloid lineage restricted progenitor cell2.04e-2566
leukocyte8.52e-25136
defensive cell1.25e-2448
phagocyte1.25e-2448
myeloid cell1.60e-22108
common myeloid progenitor1.60e-22108
hematopoietic stem cell2.73e-20168
angioblastic mesenchymal cell2.73e-20168
nongranular leukocyte3.69e-20115
hematopoietic lineage restricted progenitor cell5.35e-20120
hematopoietic oligopotent progenitor cell2.86e-19161
hematopoietic multipotent progenitor cell2.86e-19161
hematopoietic cell7.43e-19177
stuff accumulating cell2.16e-0987
intermediate monocyte4.17e-079
CD14-positive, CD16-positive monocyte4.17e-079
granulocyte6.94e-078
Uber Anatomy
Ontology termp-valuen
neural tube3.15e-2656
neural rod3.15e-2656
future spinal cord3.15e-2656
neural keel3.15e-2656
regional part of nervous system1.28e-2353
regional part of brain1.28e-2353
brain grey matter3.06e-2334
gray matter3.06e-2334
telencephalon8.65e-2334
bone marrow1.57e-2276
bone element4.51e-2282
adult organism8.48e-22114
neural plate1.06e-2182
presumptive neural plate1.06e-2182
regional part of forebrain1.37e-2141
forebrain1.37e-2141
anterior neural tube1.37e-2141
future forebrain1.37e-2141
neurectoderm1.39e-2186
regional part of telencephalon2.06e-2132
cerebral hemisphere4.98e-2132
brain9.27e-2168
future brain9.27e-2168
central nervous system1.61e-2081
hematopoietic system3.85e-1998
blood island3.85e-1998
nervous system7.98e-1989
skeletal element3.59e-1890
immune system3.75e-1793
skeletal system1.28e-16100
hemolymphoid system2.09e-16108
cerebral cortex1.05e-1525
pallium1.05e-1525
pre-chordal neural plate1.26e-1561
regional part of cerebral cortex1.12e-1322
ecto-epithelium2.54e-13104
structure with developmental contribution from neural crest1.47e-12132
neocortex6.44e-1220
neural nucleus3.31e-099
nucleus of brain3.31e-099
basal ganglion4.73e-099
nuclear complex of neuraxis4.73e-099
aggregate regional part of brain4.73e-099
collection of basal ganglia4.73e-099
cerebral subcortex4.73e-099
musculoskeletal system9.90e-08167
ectoderm-derived structure1.39e-07171
ectoderm1.39e-07171
presumptive ectoderm1.39e-07171
telencephalic nucleus2.32e-077
organ6.28e-07503


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.12.50576
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.12.03099
MA0031.10.809638
MA0038.10.60704
MA0040.12.0669
MA0041.10.521615
MA0042.11.22641
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.11.22833
MA0051.11.46692
MA0052.12.07492
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.12.64084
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.21.53797
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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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