Personal tools

Coexpression cluster:C1110: Difference between revisions

From FANTOM5_SSTAR

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

Latest revision as of 11:37, 17 September 2013


Full id: C1110_cord_mycosis_colon_embryonic_argyrophil_xeroderma_CD19



Phase1 CAGE Peaks

Hg19::chr10:133058641..133058652,-p6@TCERG1L
Hg19::chr13:28494375..28494416,+p4@PDX1
Hg19::chr13:28498703..28498710,+p@chr13:28498703..28498710
+
Hg19::chr6:31540557..31540570,+p4@LTA
Hg19::chr6:31541218..31541237,+p@chr6:31541218..31541237
+
Hg19::chr6:31541408..31541421,+p@chr6:31541408..31541421
+
Hg19::chr7:102944849..102944859,+p@chr7:102944849..102944859
+


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:0051952regulation of amine transport0.00494510345594605
GO:0002036regulation of L-glutamate transport0.00494510345594605
GO:0051953negative regulation of amine transport0.00494510345594605
GO:0051956negative regulation of amino acid transport0.00494510345594605
GO:0002037negative regulation of L-glutamate transport0.00494510345594605
GO:0051955regulation of amino acid transport0.00494510345594605
GO:0046325negative regulation of glucose import0.00847582299419329
GO:0048535lymph node development0.00847582299419329
GO:0050806positive regulation of synaptic transmission0.00847582299419329
GO:0042127regulation of cell proliferation0.00847582299419329
GO:0051971positive regulation of transmission of nerve impulse0.00847582299419329
GO:0046323glucose import0.00847582299419329
GO:0046324regulation of glucose import0.00847582299419329
GO:0031646positive regulation of neurological process0.00847582299419329
GO:0043525positive regulation of neuron apoptosis0.00889935214910135
GO:0031016pancreas development0.00926988558275227
GO:0051222positive regulation of protein transport0.00959677548276263
GO:0045840positive regulation of mitosis0.00963982957309548
GO:0015813L-glutamate transport0.00963982957309548
GO:0015800acidic amino acid transport0.00963982957309548
GO:0050804regulation of synaptic transmission0.0108424725521954
GO:0008283cell proliferation0.0108424725521954
GO:0009612response to mechanical stimulus0.0109603882890473
GO:0051969regulation of transmission of nerve impulse0.0111212430341185
GO:0045787positive regulation of progression through cell cycle0.0137271002031507
GO:0031644regulation of neurological process0.0137271002031507
GO:0043523regulation of neuron apoptosis0.0137271002031507
GO:0048522positive regulation of cellular process0.0137671221908496
GO:0051223regulation of protein transport0.0137671221908496
GO:0051402neuron apoptosis0.0137671221908496
GO:0015758glucose transport0.0137671221908496
GO:0051051negative regulation of transport0.0137671221908496
GO:0008645hexose transport0.0137671221908496
GO:0015749monosaccharide transport0.0137671221908496
GO:0048518positive regulation of biological process0.0137671221908496
GO:0019722calcium-mediated signaling0.0144486788814349
GO:0048513organ development0.0144486788814349
GO:0051050positive regulation of transport0.0144486788814349
GO:0005164tumor necrosis factor receptor binding0.0144486788814349
GO:0003704specific RNA polymerase II transcription factor activity0.0144486788814349
GO:0032813tumor necrosis factor receptor superfamily binding0.014818285051059
GO:0007088regulation of mitosis0.0236205980833195
GO:0006865amino acid transport0.0241021943152424
GO:0048731system development0.0246724218389829
GO:0006959humoral immune response0.0246724218389829
GO:0015837amine transport0.0270252262450758
GO:0048869cellular developmental process0.0287158030664027
GO:0030154cell differentiation0.0287158030664027
GO:0046942carboxylic acid transport0.0287158030664027
GO:0015849organic acid transport0.0287158030664027
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0287158030664027
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0303970611682208
GO:0051049regulation of transport0.0303970611682208
GO:0008643carbohydrate transport0.0303970611682208
GO:0048856anatomical structure development0.0306502575807213
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0360316312609124
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0360316312609124
GO:0007275multicellular organismal development0.037986522699988
GO:0009967positive regulation of signal transduction0.0383004752371746
GO:0009628response to abiotic stimulus0.0406016596967475
GO:0048534hemopoietic or lymphoid organ development0.0418624765584408
GO:0002520immune system development0.0433184679915768
GO:0006006glucose metabolic process0.0449599678871934
GO:0001775cell activation0.0475808260858078
GO:0006917induction of apoptosis0.0475808260858078
GO:0012502induction of programmed cell death0.0475808260858078
GO:0045893positive regulation of transcription, DNA-dependent0.0487658922195956
GO:0008285negative regulation of cell proliferation0.0487658922195956



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>disease_data<br>

Cell Type
Ontology termp-valuen
circulating cell5.37e-506
Uber Anatomy
Ontology termp-valuen
umbilical cord2.06e-3010
blastocyst2.06e-3010
blastula2.06e-3010
bilaminar disc2.06e-3010
inner cell mass2.06e-3010
cleaving embryo2.06e-3010
connecting stalk2.06e-3010
inner cell mass derived epiblast2.06e-3010
extraembryonic mesoderm2.06e-3010
blood1.37e-2015
haemolymphatic fluid1.37e-2015
organism substance1.37e-2015
extraembryonic structure3.48e-1324
Disease
Ontology termp-valuen
non-Hodgkin lymphoma2.58e-341
cutaneous T cell lymphoma2.58e-341
mycosis fungoides2.58e-341


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)
MA0003.10.213534
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.10.912418
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.11.04442
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
MA0073.10.126287
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.11.39213
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.11.83545
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.980834
MA0146.10.0127148
MA0147.10.768766
MA0148.11.30922
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.20.0170091
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.11.36741
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.11.34201
MA0161.10
MA0162.10.780982
MA0163.10.632664
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.184526
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1110&oldid=3068227"