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|library_id=CNhs13091
 
|library_id=CNhs13091
 
|library_id_phase_based=2:CNhs13091
 
|library_id_phase_based=2:CNhs13091
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11824
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11824
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor8.CNhs13091.11824-124F6.mm10.nobarcode.bam  
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor8.CNhs13091.11824-124F6.mm10.nobarcode.bam  
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor8.CNhs13091.11824-124F6.mm10.nobarcode.ctss.bed.gz  
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor8.CNhs13091.11824-124F6.mm10.nobarcode.ctss.bed.gz  

Revision as of 12:33, 18 May 2017


Name:Mouse hepatocyte, donor8
Species:Mouse (Mus musculus)
Library ID:CNhs13091
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stageNA
sexmale
ageNA
cell typehepatocyte
cell lineNA
companyNA
collaborationSoichi Kojima (RIKEN ASI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005803
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13091 CAGE DRX008860 DRR009732
Accession ID Mm9

Library idBAMCTSS
CNhs13091 DRZ001157 DRZ002542
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs13091

00
10
100
1000
10000
10010.126
1002-0.116
10030.0584
10040
10050
1006-0.143
1007-0.266
10080
1009-0.2
101-0.0453
10100
1011-0.137
10120
10130.566
1014-0.0874
1015-0.41
1016-0.433
10170
10180
10190
1020
10200.805
10210.0209
10220.768
10230
1024-0.14
10250.0996
10260
1027-0.0213
10280
1029-0.148
103-0.0887
10300
1031-0.615
1032-0.588
1033-0.0665
10341.051
10350
1036-0.476
10370
1038-0.193
10390.884
1040
1040-0.261
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13091

Jaspar motifP-value
MA0002.20.187
MA0003.10.67
MA0004.10.24
MA0006.10.359
MA0007.10.0503
MA0009.10.875
MA0014.10.0635
MA0017.18.16951e-23
MA0018.20.00169
MA0019.10.65
MA0024.18.81409e-5
MA0025.10.00807
MA0027.10.733
MA0028.10.52
MA0029.10.508
MA0030.10.00671
MA0031.10.00164
MA0035.20.162
MA0038.10.253
MA0039.20.941
MA0040.10.589
MA0041.10.304
MA0042.10.517
MA0043.10.807
MA0046.12.98191e-79
MA0047.21.81016e-6
MA0048.10.241
MA0050.10.542
MA0051.10.112
MA0052.10.0327
MA0055.10.275
MA0057.10.753
MA0058.10.162
MA0059.10.0321
MA0060.13.48052e-6
MA0061.10.692
MA0062.20.899
MA0065.21.2165e-16
MA0066.10.0436
MA0067.10.289
MA0068.10.782
MA0069.10.0813
MA0070.10.22
MA0071.12.78459e-5
MA0072.17.57913e-4
MA0073.10.943
MA0074.10.206
MA0076.10.893
MA0077.10.0709
MA0078.10.968
MA0079.20.202
MA0080.20.0132
MA0081.10.326
MA0083.10.00118
MA0084.10.324
MA0087.10.222
MA0088.10.207
MA0090.10.59
MA0091.10.506
MA0092.10.209
MA0093.10.278
MA0099.20.809
MA0100.10.83
MA0101.10.883
MA0102.20.292
MA0103.10.0548
MA0104.20.401
MA0105.10.186
MA0106.10.0202
MA0107.10.437
MA0108.22.57838e-6
MA0111.10.876
MA0112.23.77533e-5
MA0113.10.169
MA0114.11.06343e-22
MA0115.11.04495e-13
MA0116.10.157
MA0117.10.495
MA0119.10.0615
MA0122.10.231
MA0124.10.897
MA0125.10.576
MA0131.10.82
MA0135.10.942
MA0136.10.0405
MA0137.20.0165
MA0138.20.484
MA0139.10.337
MA0140.10.854
MA0141.11.78178e-7
MA0142.10.312
MA0143.10.186
MA0144.10.145
MA0145.10.191
MA0146.10.0727
MA0147.10.283
MA0148.13.15129e-8
MA0149.10.00388
MA0150.10.00164
MA0152.10.323
MA0153.11.08799e-56
MA0154.10.237
MA0155.10.928
MA0156.10.158
MA0157.10.00102
MA0159.12.72201e-4
MA0160.11.5975e-6
MA0162.10.553
MA0163.10.0036
MA0164.10.981
MA0258.10.00269
MA0259.10.775



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13091

Novel motifP-value
10.0769
100.173
1000.424
1010.98
1020.194
1030.00265
1040.803
1050.753
1060.174
1070.127
1080.958
1090.0679
110.103
1100.0369
1110.0103
1120.018
1130.738
1140.00183
1150.617
1160.706
1170.0578
1180.373
1190.101
120.33
1200.73
1210.793
1220.479
1230.47
1240.56
1250.719
1260.172
1270.879
1280.0706
1290.966
132.32566e-4
1300.389
1310.879
1320.593
1330.719
1340.874
1350.343
1360.777
1370.958
1380.591
1390.325
140.638
1400.117
1410.362
1420.158
1430.73
1440.474
1450.111
1460.492
1470.366
1480.738
1490.192
150.119
1500.217
1510.401
1520.175
1530.354
1540.898
1550.535
1562.90989e-4
1570.859
1580.921
1590.772
1600.25
1610.934
1620.447
1630.289
1640.045
1650.472
1660.44
1670.17
1680.899
1690.00449
170.087
180.922
190.119
20.994
200.337
210.633
220.166
230.428
240.211
250.417
260.00589
270.743
280.355
290.154
30.0857
300.935
310.393
320.133
330.316
340.84
350.156
360.115
370.0628
380.55
390.315
40.817
400.19
410.895
420.447
430.0905
440.00299
450.842
460.108
470.499
480.182
490.0387
50.0614
500.833
510.237
520.673
530.477
540.316
550.507
560.492
570.819
580.284
590.415
60.701
600.157
610.345
620.0797
630.128
640.491
650.405
660.691
670.726
680.214
690.909
70.171
700.0122
710.029
720.85
730.045
740.665
750.0062
760.657
770.456
780.0146
790.761
80.0139
800.86
810.734
820.00922
830.338
840.0287
850.0269
860.0672
870.31
880.963
890.153
90.986
900.0982
910.741
920.147
930.0937
940.7
950.197
960.36
970.477
980.532
990.223



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13091


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000109 (mouse hepatocyte sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
CL:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)