Personal tools

FF:823-25A3

From FANTOM5_SSTAR

Revision as of 18:57, 4 August 2017 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:liver, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11220
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage20 days neonate
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005799
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11220 CAGE DRX009027 DRR009901
Accession ID Mm9

Library idBAMCTSS
CNhs11220 DRZ001326 DRZ002709
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

CNhs11220

00
10
100
1000
10000.0978
10010.0967
1002-0.116
10030.0704
10040
10050
1006-0.088
1007-0.0636
10080
10090.0921
1010.00512
10100
1011-0.2
10120
10130.381
1014-0.0851
1015-0.382
1016-0.282
10170
10180
10190
1020
10200
1021-0.0487
10220.556
10230
10240
10250.577
10260
10270
10280
10290.204
103-0.0578
10300
1031-0.00412
1032-0.216
1033-0.0665
10340.822
10350
1036-0.217
10370
1038-0.043
10390.717
1040
1040-0.139
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: CNhs11220

Jaspar motifP-value
MA0002.20.313
MA0003.10.517
MA0004.10.562
MA0006.10.216
MA0007.10.173
MA0009.10.43
MA0014.10.196
MA0017.15.60497e-27
MA0018.25.96061e-6
MA0019.10.597
MA0024.10.126
MA0025.10.0476
MA0027.10.88
MA0028.10.635
MA0029.10.347
MA0030.10.00153
MA0031.10.00555
MA0035.20.118
MA0038.10.718
MA0039.20.271
MA0040.10.332
MA0041.10.896
MA0042.10.992
MA0043.10.136
MA0046.14.14036e-95
MA0047.28.99945e-9
MA0048.10.237
MA0050.10.00212
MA0051.18.02751e-4
MA0052.10.0111
MA0055.10.171
MA0057.10.556
MA0058.10.387
MA0059.10.11
MA0060.10.156
MA0061.10.562
MA0062.20.996
MA0065.21.12927e-17
MA0066.10.0498
MA0067.10.071
MA0068.10.737
MA0069.10.208
MA0070.10.422
MA0071.13.05012e-5
MA0072.18.76728e-6
MA0073.10.744
MA0074.10.231
MA0076.10.744
MA0077.10.0365
MA0078.10.53
MA0079.20.345
MA0080.20.845
MA0081.10.837
MA0083.10.0202
MA0084.10.869
MA0087.10.211
MA0088.10.365
MA0090.10.724
MA0091.10.599
MA0092.10.135
MA0093.10.565
MA0099.20.492
MA0100.10.222
MA0101.10.715
MA0102.20.199
MA0103.10.194
MA0104.20.968
MA0105.10.172
MA0106.10.0292
MA0107.10.926
MA0108.27.02523e-4
MA0111.10.748
MA0112.26.35006e-6
MA0113.10.662
MA0114.11.89255e-27
MA0115.11.09815e-11
MA0116.10.183
MA0117.10.982
MA0119.10.00671
MA0122.10.302
MA0124.10.488
MA0125.10.512
MA0131.10.941
MA0135.10.488
MA0136.10.237
MA0137.20.179
MA0138.20.507
MA0139.10.175
MA0140.10.823
MA0141.15.85751e-7
MA0142.10.0529
MA0143.10.342
MA0144.10.45
MA0145.10.0834
MA0146.10.145
MA0147.10.934
MA0148.17.3925e-12
MA0149.10.0161
MA0150.10.00625
MA0152.10.46
MA0153.13.57731e-62
MA0154.10.171
MA0155.10.548
MA0156.10.683
MA0157.10.00251
MA0159.18.08258e-4
MA0160.12.74681e-5
MA0162.10.616
MA0163.10.00268
MA0164.10.792
MA0258.10.00421
MA0259.10.672



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: CNhs11220

Novel motifP-value
10.089
100.231
1000.706
1010.902
1020.109
1030.0114
1040.798
1050.646
1060.0862
1070.071
1080.289
1090.0391
110.104
1100.0258
1110.0723
1120.004
1130.922
1140.0295
1150.755
1160.687
1170.0727
1180.277
1190.119
120.636
1200.245
1210.606
1220.335
1230.164
1240.67
1250.393
1260.178
1270.627
1280.0454
1290.709
132.23115e-5
1300.997
1310.307
1320.358
1330.449
1340.815
1350.555
1360.368
1370.978
1380.361
1390.624
140.397
1400.0306
1410.665
1420.122
1430.829
1440.638
1450.0482
1460.398
1470.441
1480.263
1490.301
150.192
1500.143
1510.547
1520.0887
1530.233
1540.83
1550.6
1560.378
1570.657
1580.993
1590.726
1600.151
1610.985
1620.335
1630.482
1640.0415
1650.458
1660.233
1670.414
1680.902
1697.85895e-4
170.051
180.934
190.0163
20.862
200.43
210.305
220.137
230.309
240.316
250.708
260.00146
270.83
280.463
290.29
30.0632
300.89
310.383
320.208
330.314
340.873
350.683
360.0533
370.0668
380.199
390.297
40.917
400.116
410.517
420.379
430.0623
440.179
450.634
460.119
470.429
480.164
490.0449
50.136
500.641
510.323
520.372
530.621
540.507
550.586
560.428
570.996
580.286
590.304
60.667
600.163
610.256
620.133
630.11
640.682
650.161
660.779
670.889
680.141
690.828
70.138
700.105
710.0573
720.627
730.0797
740.792
750.0302
760.827
770.513
780.0177
790.856
80.0166
800.606
810.64
820.0521
830.529
840.144
850.0424
860.163
870.764
880.644
890.0562
90.816
900.0869
910.346
920.304
930.0733
940.686
950.282
960.2
970.419
980.585
990.117



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: CNhs11220


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
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)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011429 (mouse liver- neonate N20 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
UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:823-25A3&oldid=4342897"