Personal tools

Coexpression cluster:C4803: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0553503591673705,

Latest revision as of 14:20, 17 September 2013


Full id: C4803_CD14_Mast_serous_Eosinophils_cord_ductus_epididymis



Phase1 CAGE Peaks

Hg19::chr9:132251080..132251099,+p3@LOC100506190
Hg19::chr9:132251115..132251147,+p2@LOC100506190
Hg19::chr9:132251160..132251219,+p1@ENST00000419300


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>


Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm4.62e-16203
hematopoietic system6.76e-1598
blood island6.76e-1598
bone marrow1.18e-1476
hemolymphoid system2.08e-14108
bone element1.09e-1382
skeletal element1.81e-1290
immune system5.62e-1293
skeletal system7.94e-11100
mesoderm2.80e-09315
mesoderm-derived structure2.80e-09315
presumptive mesoderm2.80e-09315
musculoskeletal system1.61e-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)
MA0003.19.41405
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.15.56064
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0116.14.65896
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
MA0136.10.948776
MA0139.15.09957
MA0140.10.894983
MA0141.12.84752
MA0142.11.12317
MA0143.11.00455
MA0144.12.26598
MA0145.10.752137
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.13.19371
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.13.52399
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.23.70709
MA0099.22.08754
MA0079.24.10519
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
BRCA1#672320.18423064322380.0001215704860271640.00164571613612326
CCNT2#90536.336201576962630.003930750035764890.0191395217952002
CEBPB#105137.971147625824820.001974187055288560.0115884735761736
CTCF#1066435.360256373075030.0064925092527670.0281684601964828
E2F1#186934.907389214879320.008460985347239390.0328155395380398
E2F4#1874312.66806031528440.0004917987006298980.0043941281970302
E2F6#187635.017155731697390.00791769806886330.0324752177125246
EBF1#187938.9064668465690.00141523283560980.00919645981323123
EGR1#195834.988179094810140.008056488137383440.0322849959550376
ELF1#199734.258097958807540.01295179875054610.0465347774084314
ELK4#2005316.2356816584680.0002336043955745990.00256517815891237
EP300#203336.77394172622320.003216880500103790.0168624665002178
ESR1#2099330.76860329615453.43136389821584e-050.000680015586652303
FOS#235338.99795530889440.001372499272417130.00902546603148045
FOSL2#2355316.93020060456170.0002060162053171620.00244168480108024
FOXA1#3169311.08141974938550.000734755275698670.00584841904113203
GATA3#2625327.2365163572064.94721007899563e-050.00085571658403482
GTF2F1#2962312.73966087675770.0004835525047438590.00436224756352629
HMGN3#932438.178547723350590.001827766942164210.0109348772224717
JUN#3725312.51282919233630.0005103313992726250.00446610533003466
JUNB#3726330.61063265982113.4847716247536e-050.000683081951422
JUND#372736.994663941871030.002921845042734990.0157800483203123
MXI1#460139.96157162875930.001011470541259020.00723987196618128
NR2C2#7182221.74307393682720.002762207975496010.0151410401906696
NR3C1#2908314.9730233311730.0002978331194675480.00310557040376111
RAD21#5885310.35503389545630.0009004912073565420.00669321765035299
SMARCB1#6598318.25271578115740.000164397760679890.00204156215548716
SMC3#9126315.04493284493280.0002935825420371870.00311062870120947
STAT3#6774310.51946499715420.0008589184530415310.00646146973400594
TCF7L2#6934310.77017656313730.0008003181298398380.00617999446671666
TRIM28#10155318.59052504526250.0001555969297255280.00198223807557994
USF1#739136.361499277207960.00388404057290560.0191360181806627
YY1#752834.911170749853860.008441455341808260.0331534730160617



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.