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Coexpression cluster:C1427: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;10.6361,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;5.69366,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.959858,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;1.02896,MA0103.1;0.381434,MA0105.1;3.35204,MA0106.1;0.70837,MA0107.1;0.857383,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;1.84113,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;2.62599,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;1.47313,MA0145.1;1.16614,MA0146.1;7.58496,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;6.1078,MA0138.2;3.01409,MA0002.2;1.3092,MA0137.2;1.06611,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;1.65732,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.92418,MA0155.1;4.31015,MA0156.1;1.07131,MA0157.1;0.810597,MA0158.1;0,MA0159.1;1.57484,MA0160.1;0.600559,MA0161.1;0,MA0162.1;2.97671,MA0163.1;3.77571,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;7.99388,MA0102.2;1.58513,MA0258.1;1.43672,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:55, 22 January 2013


Full id: C1427_Mast_Monocytederived_granulocyte_CD14_testicular_Macrophage_acute



Phase1 CAGE Peaks

Hg19::chr17:10101893..10101900,-p21@GAS7
Hg19::chr17:10101909..10101934,-p2@GAS7
Hg19::chr17:10101952..10101963,-p14@GAS7
Hg19::chr17:10102156..10102163,-p23@GAS7
Hg19::chr17:10102176..10102203,-p4@GAS7
Hg19::chr17:10102207..10102229,-p7@GAS7


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

No GOStat results

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 leukocyte7.96e-3672
granulocyte monocyte progenitor cell1.26e-3267
myeloid lineage restricted progenitor cell1.05e-3066
monopoietic cell1.52e-3059
monocyte1.52e-3059
monoblast1.52e-3059
promonocyte1.52e-3059
defensive cell2.07e-3048
phagocyte2.07e-3048
macrophage dendritic cell progenitor2.62e-2961
classical monocyte1.67e-2642
CD14-positive, CD16-negative classical monocyte1.67e-2642
stuff accumulating cell3.76e-1987
myeloid cell1.49e-18108
common myeloid progenitor1.49e-18108
leukocyte4.25e-16136
nongranular leukocyte1.12e-13115
hematopoietic lineage restricted progenitor cell1.33e-13120
hematopoietic stem cell1.54e-10168
angioblastic mesenchymal cell1.54e-10168
hematopoietic cell2.48e-10177
hematopoietic oligopotent progenitor cell9.58e-10161
hematopoietic multipotent progenitor cell9.58e-10161
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.96e-2898
blood island5.96e-2898
hemolymphoid system6.48e-26108
bone marrow1.00e-2576
adult organism2.74e-24114
immune system2.17e-2393
bone element3.43e-2382
skeletal element4.55e-1890
skeletal system4.35e-16100
central nervous system3.73e-1381
neural tube4.31e-1356
neural rod4.31e-1356
future spinal cord4.31e-1356
neural keel4.31e-1356
regional part of nervous system1.45e-1253
regional part of brain1.45e-1253
tissue2.98e-12773
neural plate5.05e-1282
presumptive neural plate5.05e-1282
neurectoderm9.45e-1286
brain1.10e-1168
future brain1.10e-1168
regional part of forebrain2.57e-1141
forebrain2.57e-1141
anterior neural tube2.57e-1141
future forebrain2.57e-1141
organ1.02e-10503
nervous system3.61e-1089
telencephalon5.64e-1034
pre-chordal neural plate1.79e-0961
brain grey matter1.90e-0934
gray matter1.90e-0934
cerebral hemisphere2.42e-0932
regional part of telencephalon4.60e-0932
neocortex2.66e-0820
regional part of cerebral cortex4.35e-0822
mesoderm4.88e-08315
mesoderm-derived structure4.88e-08315
presumptive mesoderm4.88e-08315
cerebral cortex9.89e-0825
pallium9.89e-0825
lateral plate mesoderm1.62e-07203
musculoskeletal system3.60e-07167
germ layer4.37e-07560
germ layer / neural crest4.37e-07560
embryonic tissue4.37e-07560
presumptive structure4.37e-07560
germ layer / neural crest derived structure4.37e-07560
epiblast (generic)4.37e-07560
embryonic structure8.63e-07564


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)
MA0003.110.6361
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.15.69366
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.959858
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.13.35204
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.12.62599
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.11.47313
MA0145.11.16614
MA0146.17.58496
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.26.1078
MA0138.23.01409
MA0002.21.3092
MA0137.21.06611
MA0104.20.26661
MA0047.20.695777
MA0112.21.65732
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.92418
MA0155.14.31015
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.11.57484
MA0160.10.600559
MA0161.10
MA0162.12.97671
MA0163.13.77571
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.99388
MA0102.21.58513
MA0258.11.43672
MA0259.10.336472
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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