Personal tools

Coexpression cluster:C1852: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:53, 17 September 2013


Full id: C1852_Neutrophils_CD19_CD4_Peripheral_Eosinophils_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr1:227127664..227127698,-p@chr1:227127664..227127698
-
Hg19::chr1:40840182..40840198,-p@chr1:40840182..40840198
-
Hg19::chr1:40840233..40840259,-p@chr1:40840233..40840259
-
Hg19::chr1:40851288..40851322,-p@chr1:40851288..40851322
-
Hg19::chr1:40851848..40851881,+p@chr1:40851848..40851881
+


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
leukocyte4.18e-78136
hematopoietic stem cell3.34e-69168
angioblastic mesenchymal cell3.34e-69168
hematopoietic cell1.16e-67177
hematopoietic oligopotent progenitor cell9.11e-64161
hematopoietic multipotent progenitor cell9.11e-64161
nongranular leukocyte1.37e-61115
hematopoietic lineage restricted progenitor cell1.92e-59120
lymphocyte3.74e-4253
common lymphoid progenitor3.74e-4253
lymphoid lineage restricted progenitor cell1.42e-4152
nucleate cell6.38e-4055
myeloid leukocyte2.76e-2672
myeloid cell7.01e-24108
common myeloid progenitor7.01e-24108
T cell3.92e-2125
pro-T cell3.92e-2125
mature alpha-beta T cell1.47e-2018
alpha-beta T cell1.47e-2018
immature T cell1.47e-2018
mature T cell1.47e-2018
immature alpha-beta T cell1.47e-2018
classical monocyte2.03e-2042
CD14-positive, CD16-negative classical monocyte2.03e-2042
granulocyte monocyte progenitor cell4.18e-2067
macrophage dendritic cell progenitor1.93e-1961
myeloid lineage restricted progenitor cell4.91e-1866
monopoietic cell7.69e-1859
monocyte7.69e-1859
monoblast7.69e-1859
promonocyte7.69e-1859
lymphocyte of B lineage9.11e-1824
pro-B cell9.11e-1824
defensive cell1.90e-1648
phagocyte1.90e-1648
mesenchymal cell3.40e-15354
connective tissue cell3.04e-14361
B cell1.18e-1314
CD8-positive, alpha-beta T cell4.21e-1311
motile cell2.25e-11386
granulocyte1.57e-108
intermediate monocyte6.31e-109
CD14-positive, CD16-positive monocyte6.31e-109
blood cell1.03e-0811
CD4-positive, alpha-beta T cell1.12e-086
multi fate stem cell1.51e-07427
stem cell4.17e-07441
somatic stem cell4.69e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.74e-3498
blood island4.74e-3498
hemolymphoid system3.04e-31108
immune system2.34e-2093
bone marrow3.74e-1876
bone element1.49e-1682
blood2.04e-1415
haemolymphatic fluid2.04e-1415
organism substance2.04e-1415
skeletal element8.54e-1490
connective tissue2.10e-13371
skeletal system1.07e-11100
lateral plate mesoderm2.41e-07203


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)
MA0003.10.136928
MA0004.10.626788
MA0006.14.0459
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.08296
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.11.8711
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
MA0144.10.356507
MA0145.10.442008
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.0439995
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.20.0850863
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
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
BCL11A#53335211.34778204144280.01157056933741320.0422893680150515
CHD2#110636.206413700470110.007774550126275590.0319583674041837
EP300#203345.419153380978560.00209386927943890.0121200251441179
GTF2F1#296237.643796526054590.00428415496412050.0203471059707949
JUND#372745.595731153496820.001849593301755460.0109364023575858
MEF2A#4205414.99458472771523.876195075647e-050.000728235181697242
MEF2C#4208216.52454179704960.005579850077982050.0252460235798799
NFKB1#479055.488063424193840.0002008162847462320.00239172676047573
POU2F2#545247.284899246194020.0006631223288743860.00542672252823319
SPI1#668858.204323508522732.68916109982495e-050.000574812312944367
TAF1#687253.343046285745290.002394600090870310.0135454497584577
TBP#690853.706770687096390.001428755106721120.0091939466784256
YY1#752843.928936599883080.007193866269917620.0298474574671828



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1852&oldid=3068969"