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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.113253630556904,0.

Latest revision as of 11:49, 17 September 2013


Full id: C1660_CD14_substantia_corpus_globus_thalamus_optic_spinal



Phase1 CAGE Peaks

Hg19::chr12:121570672..121570772,+p1@P2RX7
Hg19::chr17:9939865..9939889,-p5@GAS7
Hg19::chr17:9939908..9939926,-p8@GAS7
Hg19::chr18:21166841..21166864,-p3@NPC1
Hg19::chr18:21977258..21977276,+p2@LOC100289533


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:0046686response to cadmium ion0.0174762390536148
GO:0004931ATP-gated cation channel activity0.0174762390536148
GO:0033344cholesterol efflux0.0174762390536148
GO:0015248sterol transporter activity0.0174762390536148
GO:0007041lysosomal transport0.0174762390536148
GO:0008206bile acid metabolic process0.0174762390536148
GO:0042632cholesterol homeostasis0.0174762390536148
GO:0055092sterol homeostasis0.0174762390536148
GO:0008158hedgehog receptor activity0.0174762390536148
GO:0055088lipid homeostasis0.0174762390536148
GO:0015918sterol transport0.0174762390536148
GO:0030301cholesterol transport0.0174762390536148
GO:0007034vacuolar transport0.0224008173644822
GO:0031902late endosome membrane0.0241260387178422
GO:0010038response to metal ion0.0271716563837915
GO:0010035response to inorganic substance0.0302408687262414
GO:0005887integral to plasma membrane0.0302408687262414
GO:0005765lysosomal membrane0.0302408687262414
GO:0005770late endosome0.0302408687262414
GO:0031226intrinsic to plasma membrane0.0302408687262414
GO:0005774vacuolar membrane0.0323758025332802
GO:0048471perinuclear region of cytoplasm0.0323758025332802
GO:0044437vacuolar part0.0323758025332802
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0348969376001375
GO:0044440endosomal part0.038241615401665
GO:0010008endosome membrane0.038241615401665
GO:0022892substrate-specific transporter activity0.038241615401665
GO:0005319lipid transporter activity0.0398540249595936
GO:0007050cell cycle arrest0.0404779378738486



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
defensive cell6.71e-3948
phagocyte6.71e-3948
myeloid leukocyte2.40e-3772
monopoietic cell2.40e-3659
monocyte2.40e-3659
monoblast2.40e-3659
promonocyte2.40e-3659
macrophage dendritic cell progenitor9.86e-3661
classical monocyte4.75e-3542
CD14-positive, CD16-negative classical monocyte4.75e-3542
granulocyte monocyte progenitor cell3.43e-3267
myeloid lineage restricted progenitor cell9.09e-3266
stuff accumulating cell5.11e-2687
leukocyte2.60e-22136
myeloid cell8.93e-21108
common myeloid progenitor8.93e-21108
nongranular leukocyte4.96e-20115
hematopoietic lineage restricted progenitor cell2.06e-17120
hematopoietic stem cell3.19e-15168
angioblastic mesenchymal cell3.19e-15168
hematopoietic oligopotent progenitor cell1.96e-13161
hematopoietic multipotent progenitor cell1.96e-13161
hematopoietic cell2.12e-13177
intermediate monocyte3.83e-079
CD14-positive, CD16-positive monocyte3.83e-079
Uber Anatomy
Ontology termp-valuen
adult organism1.85e-48114
hemolymphoid system1.47e-32108
hematopoietic system8.17e-3298
blood island8.17e-3298
bone marrow3.72e-2976
immune system3.19e-2893
bone element4.06e-2682
neural tube5.35e-2656
neural rod5.35e-2656
future spinal cord5.35e-2656
neural keel5.35e-2656
regional part of nervous system1.03e-2353
regional part of brain1.03e-2353
skeletal element1.52e-2190
central nervous system5.36e-1981
skeletal system1.37e-18100
regional part of forebrain1.51e-1841
forebrain1.51e-1841
anterior neural tube1.51e-1841
future forebrain1.51e-1841
brain1.91e-1868
future brain1.91e-1868
brain grey matter4.07e-1634
gray matter4.07e-1634
nervous system4.75e-1689
telencephalon5.48e-1634
neural plate8.67e-1582
presumptive neural plate8.67e-1582
regional part of telencephalon1.52e-1432
cerebral hemisphere2.36e-1432
neurectoderm3.20e-1386
regional part of cerebral cortex2.82e-1122
pre-chordal neural plate2.03e-1061
neocortex4.95e-1020
lateral plate mesoderm6.53e-10203
cerebral cortex7.02e-1025
pallium7.02e-1025
ecto-epithelium8.78e-10104
organ3.00e-09503
posterior neural tube1.18e-0815
chordal neural plate1.18e-0815
neural nucleus2.51e-089
nucleus of brain2.51e-089
structure with developmental contribution from neural crest2.91e-08132
germ layer7.63e-08560
germ layer / neural crest7.63e-08560
embryonic tissue7.63e-08560
presumptive structure7.63e-08560
germ layer / neural crest derived structure7.63e-08560
epiblast (generic)7.63e-08560
basal ganglion1.50e-079
nuclear complex of neuraxis1.50e-079
aggregate regional part of brain1.50e-079
collection of basal ganglia1.50e-079
cerebral subcortex1.50e-079
embryonic structure2.02e-07564
segmental subdivision of nervous system2.81e-0713
musculoskeletal system8.38e-07167


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)
MA0003.10.280184
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.11.48918
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.12.43492
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.12.02769
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.11.74965
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.143698
MA0146.10.143081
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.83106
MA0137.22.08722
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.168633
MA0164.13.15573
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
SREBF2#6721187.38865248226950.01139099762298490.0417440752569185



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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