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Coexpression cluster:C4448: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.0834661,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;2.18164,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;0.273764,MA0146.1;1.16674,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.9924,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 22:04, 22 January 2013


Full id: C4448_Neutrophils_pons_brain_frontal_Eosinophils_Mast_spinal



Phase1 CAGE Peaks

Hg19::chr5:108745603..108745631,-p1@PJA2
Hg19::chr6:122792919..122792970,-p1@SERINC1
Hg19::chr6:122792978..122792992,-p2@SERINC1


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:0032329serine transport0.00238428140252734
GO:0015825L-serine transport0.00238428140252734
GO:0022889serine transmembrane transporter activity0.00238428140252734
GO:0015194L-serine transmembrane transporter activity0.00238428140252734
GO:0005789endoplasmic reticulum membrane0.0025456993930067
GO:0042175nuclear envelope-endoplasmic reticulum network0.0025456993930067
GO:0044432endoplasmic reticulum part0.00270600274992411
GO:0006658phosphatidylserine metabolic process0.00476814168412872
GO:0015807L-amino acid transport0.00529777923387416
GO:0005783endoplasmic reticulum0.00575482801364196
GO:0015804neutral amino acid transport0.00617501311531734
GO:0012505endomembrane system0.00617501311531734
GO:0015175neutral amino acid transmembrane transporter activity0.00623443615742896
GO:0015179L-amino acid transmembrane transporter activity0.0106759301763204
GO:0031090organelle membrane0.0106759301763204
GO:0015171amino acid transmembrane transporter activity0.0185258503936613
GO:0006665sphingolipid metabolic process0.0185258503936613
GO:0006865amino acid transport0.0185258503936613
GO:0015837amine transport0.0200384602203091
GO:0046943carboxylic acid transmembrane transporter activity0.0200384602203091
GO:0046942carboxylic acid transport0.0200384602203091
GO:0015849organic acid transport0.0200384602203091
GO:0005342organic acid transmembrane transporter activity0.0200384602203091
GO:0006650glycerophospholipid metabolic process0.0200384602203091
GO:0051347positive regulation of transferase activity0.027268406000498
GO:0045211postsynaptic membrane0.027268406000498
GO:0044456synapse part0.0283682184882672
GO:0005886plasma membrane0.0352423033661863
GO:0006644phospholipid metabolic process0.0352423033661863
GO:0051338regulation of transferase activity0.0368541894013872
GO:0044446intracellular organelle part0.0368541894013872
GO:0044422organelle part0.0368541894013872
GO:0043085positive regulation of catalytic activity0.0368541894013872
GO:0006643membrane lipid metabolic process0.0379968989070936
GO:0044444cytoplasmic part0.0422762736071943
GO:0000139Golgi membrane0.0480896116943764



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
adult organism1.43e-34114
neural tube6.52e-2356
neural rod6.52e-2356
future spinal cord6.52e-2356
neural keel6.52e-2356
regional part of nervous system8.70e-2253
regional part of brain8.70e-2253
central nervous system1.03e-2081
regional part of forebrain1.30e-2041
forebrain1.30e-2041
anterior neural tube1.30e-2041
future forebrain1.30e-2041
brain1.19e-1968
future brain1.19e-1968
nervous system1.29e-1889
telencephalon6.54e-1734
brain grey matter8.61e-1734
gray matter8.61e-1734
cerebral hemisphere9.10e-1632
regional part of telencephalon1.11e-1532
neural plate5.78e-1482
presumptive neural plate5.78e-1482
regional part of cerebral cortex1.67e-1322
neurectoderm5.74e-1386
neocortex2.25e-1220
cerebral cortex7.40e-1225
pallium7.40e-1225
pre-chordal neural plate3.16e-1161
structure with developmental contribution from neural crest1.15e-10132
ectoderm-derived structure1.98e-09171
ectoderm1.98e-09171
presumptive ectoderm1.98e-09171
ecto-epithelium2.00e-09104
organ5.80e-08503


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.12.18164
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
E2F1#186934.907389214879320.008460985347239390.0327001757273558
ELF1#199734.258097958807540.01295179875054610.0464277641911201
GABPB1#255337.067683836182170.002832212825417420.0154630913938925
IRF1#365937.63716375356390.002244692747297240.0128576463464584
RFX5#5993312.04791082719510.0005717246050312580.00486003141989741
SIN3A#2594235.408884726815140.006318961977991520.0277872029481876
SP1#666735.69838137814090.005403962701712170.0247558759805297
TRIM28#10155212.39368336350830.008368344129438470.0329381733826194
YY1#752834.911170749853860.008441455341808260.0330726321207605



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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