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|library_id=CNhs13196
|library_id=CNhs13196
|library_id_phase_based=2:CNhs13196
|library_id_phase_based=2:CNhs13196
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11825
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11825
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm10.nobarcode.ctss.bed.gz

Revision as of 21:33, 18 May 2017


Name:Mouse hepatic Stellate Cells (lipocyte), donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13196
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stageNA
sexmale
ageNA
cell typeadipocyte, lipocyte of liver
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  SAMD00005887
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13196 CAGE DRX008856 DRR009728
Accession ID Mm9

Library idBAMCTSS
CNhs13196 DRZ001153 DRZ002538
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

CNhs13196

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.0941
1003-0.123
10040
10050
10060.00388
1007-0.144
10080
10090.0795
101-0.0954
10100
1011-0.298
10120
10130.425
1014-0.0874
1015-0.316
1016-0.379
10170
10180
10190
1020
10200
10210.179
10220.485
10230
10240.13
10250.397
10260
10270
10280
1029-0.176
103-0.0787
10300
10310.0899
1032-0.227
1033-0.0665
10340.539
10350
1036-0.369
10370
10380.0498
10390.773
1040
1040-0.0865
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: CNhs13196

Jaspar motifP-value
MA0002.20.0803
MA0003.10.205
MA0004.10.865
MA0006.10.168
MA0007.10.412
MA0009.10.873
MA0014.10.195
MA0017.15.7771e-17
MA0018.20.00157
MA0019.10.598
MA0024.11.25216e-4
MA0025.10.09
MA0027.10.795
MA0028.10.889
MA0029.10.59
MA0030.10.0436
MA0031.10.00479
MA0035.20.0353
MA0038.10.654
MA0039.20.311
MA0040.10.196
MA0041.10.24
MA0042.10.552
MA0043.10.26
MA0046.13.97466e-67
MA0047.24.53176e-6
MA0048.10.608
MA0050.14.09488e-4
MA0051.13.75642e-5
MA0052.10.303
MA0055.10.465
MA0057.10.415
MA0058.10.603
MA0059.10.226
MA0060.11.16885e-4
MA0061.10.129
MA0062.20.808
MA0065.25.33758e-13
MA0066.10.157
MA0067.10.325
MA0068.10.417
MA0069.10.465
MA0070.10.411
MA0071.17.92163e-5
MA0072.16.66368e-6
MA0073.10.916
MA0074.10.325
MA0076.10.55
MA0077.10.193
MA0078.10.999
MA0079.20.393
MA0080.20.139
MA0081.10.605
MA0083.10.305
MA0084.10.743
MA0087.10.792
MA0088.10.352
MA0090.10.268
MA0091.10.862
MA0092.10.151
MA0093.10.9
MA0099.20.579
MA0100.10.184
MA0101.10.211
MA0102.20.177
MA0103.10.427
MA0104.20.75
MA0105.10.0185
MA0106.10.274
MA0107.10.251
MA0108.20.656
MA0111.10.615
MA0112.21.40006e-4
MA0113.10.528
MA0114.11.09405e-15
MA0115.19.17531e-8
MA0116.10.191
MA0117.10.648
MA0119.10.021
MA0122.10.811
MA0124.10.725
MA0125.10.195
MA0131.10.594
MA0135.10.276
MA0136.10.259
MA0137.27.45415e-4
MA0138.20.396
MA0139.10.175
MA0140.10.566
MA0141.16.26011e-5
MA0142.10.124
MA0143.10.437
MA0144.10.0138
MA0145.10.0346
MA0146.10.246
MA0147.10.853
MA0148.16.03729e-7
MA0149.10.0153
MA0150.10.00847
MA0152.10.355
MA0153.11.82777e-52
MA0154.10.066
MA0155.10.706
MA0156.10.431
MA0157.10.00106
MA0159.10.00109
MA0160.13.27555e-4
MA0162.10.176
MA0163.15.97778e-4
MA0164.10.515
MA0258.10.0111
MA0259.10.534



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: CNhs13196

Novel motifP-value
10.0986
100.202
1000.762
1010.664
1020.215
1030.00416
1040.241
1050.404
1060.0213
1070.0296
1080.886
1090.0232
110.0508
1100.0792
1110.0491
1120.00569
1130.632
1140.0492
1150.345
1160.698
1170.126
1180.702
1190.115
120.383
1200.98
1210.188
1220.621
1230.418
1240.561
1250.529
1260.453
1270.623
1280.00676
1290.736
137.90275e-4
1300.979
1310.107
1320.533
1330.745
1340.547
1350.366
1360.46
1370.763
1380.534
1390.716
140.441
1400.537
1410.131
1420.329
1430.506
1440.95
1450.133
1460.534
1470.52
1480.985
1490.133
150.177
1500.22
1510.59
1520.0379
1530.297
1540.597
1550.956
1560.00489
1570.872
1580.482
1590.25
1600.253
1610.419
1620.438
1630.255
1640.117
1650.186
1660.159
1670.527
1680.695
1690.00408
170.0162
180.828
190.0283
20.479
200.874
210.726
220.131
230.49
240.106
250.65
260.00767
270.695
280.542
290.457
30.0574
300.522
310.272
320.0969
330.272
340.642
350.711
360.0273
370.0302
380.409
390.304
40.934
400.0642
410.687
420.357
430.0742
440.0259
450.626
460.122
470.428
480.182
490.0817
50.166
500.547
510.357
520.275
530.69
540.383
550.519
560.346
570.818
580.38
590.076
60.853
600.0827
610.375
620.145
630.0969
640.518
650.159
660.794
670.879
680.0712
690.772
70.191
700.0254
710.0568
720.58
730.029
740.183
750.0383
760.887
770.257
780.0866
790.744
80.00802
800.49
810.608
820.0431
830.228
840.09
850.0385
860.215
870.0913
880.79
890.0382
90.954
900.183
910.286
920.0751
930.082
940.898
950.171
960.931
970.503
980.493
990.16



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: CNhs13196


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)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0000632 (hepatic stellate cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0002384 (connective tissue)
0000479 (tissue)
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)
0000077 (hepatic stellate cell sample)
0011461 (Mouse hepatic Stellate Cells (lipocyte) 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)

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