Personal tools

FF:684-20A8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008887
|DRA_sample_Accession=CAGE@SAMD00005319
|accession_numbers=CAGE;DRX009024;DRR009898;DRZ001323;DRZ002706
|accession_numbers=CAGE;DRX009024;DRR009898;DRZ001323;DRZ002706
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423

Revision as of 21:59, 31 July 2014


Name:liver, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11101
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage6 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  SAMD00005319
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11101 CAGE DRX009024 DRR009898
Accession ID Mm9

Library idBAMCTSS
CNhs11101 DRZ001323 DRZ002706
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11101

00
10
100
1000
10000
10010.659
10020.161
10030.3
10040
10050.348
10060.0455
10070.13
10080
10090.197
1010.0375
10100
1011-0.108
10120.49
10130.273
10140.387
1015-0.172
1016-0.0783
10170
10180
10190
1020
10200
10210
10220.289
10230
10240.0799
10250.428
10260
10270
10280
10290.949
1030.387
10300.588
10310.241
1032-0.246
10330
10340.739
10350
10360.0388
10370
10380.205
10390.324
1040
1040-0.121
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: CNhs11101

Jaspar motifP-value
MA0002.20.645
MA0003.10.406
MA0004.10.953
MA0006.10.373
MA0007.10.362
MA0009.10.336
MA0014.10.575
MA0017.17.18432e-8
MA0018.21.0695e-7
MA0019.10.82
MA0024.10.363
MA0025.10.126
MA0027.10.887
MA0028.10.038
MA0029.10.879
MA0030.10.805
MA0031.10.964
MA0035.20.481
MA0038.10.0173
MA0039.20.00762
MA0040.10.38
MA0041.10.134
MA0042.10.461
MA0043.15.94727e-4
MA0046.12.32812e-12
MA0047.20.127
MA0048.10.0732
MA0050.10.237
MA0051.10.655
MA0052.10.00279
MA0055.10.695
MA0057.10.883
MA0058.10.944
MA0059.10.0724
MA0060.14.25377e-8
MA0061.10.247
MA0062.24.27898e-4
MA0065.23.98505e-5
MA0066.10.0118
MA0067.10.146
MA0068.10.541
MA0069.10.214
MA0070.10.627
MA0071.10.0246
MA0072.10.068
MA0073.10.693
MA0074.10.327
MA0076.10.0064
MA0077.10.0226
MA0078.10.947
MA0079.20.0343
MA0080.20.0126
MA0081.10.212
MA0083.10.132
MA0084.10.485
MA0087.10.164
MA0088.10.471
MA0090.10.947
MA0091.10.262
MA0092.10.102
MA0093.10.972
MA0099.20.0411
MA0100.10.477
MA0101.10.865
MA0102.20.995
MA0103.10.393
MA0104.20.805
MA0105.18.28206e-6
MA0106.10.081
MA0107.10.944
MA0108.24.21709e-7
MA0111.10.497
MA0112.22.179e-6
MA0113.10.372
MA0114.16.7835e-8
MA0115.11.39818e-4
MA0116.10.0157
MA0117.10.968
MA0119.10.022
MA0122.10.0475
MA0124.10.913
MA0125.10.347
MA0131.10.672
MA0135.10.00165
MA0136.14.73062e-6
MA0137.20.227
MA0138.20.908
MA0139.10.46
MA0140.10.0771
MA0141.17.50605e-4
MA0142.10.732
MA0143.10.183
MA0144.10.75
MA0145.10.745
MA0146.10.917
MA0147.10.949
MA0148.10.00679
MA0149.10.0599
MA0150.10.448
MA0152.10.371
MA0153.17.7018e-11
MA0154.10.0061
MA0155.10.722
MA0156.10.00565
MA0157.10.35
MA0159.10.0117
MA0160.10.0677
MA0162.10.457
MA0163.14.6319e-5
MA0164.10.428
MA0258.10.0021
MA0259.10.819



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: CNhs11101

Novel motifP-value
10.0685
100.054
1000.686
1010.717
1020.442
1030.00299
1040.801
1050.543
1060.0181
1070.00981
1080.715
1090.321
110.171
1100.0608
1110.0404
1120.0198
1130.662
1140.0384
1150.398
1160.928
1170.0162
1180.179
1190.162
120.669
1200.967
1210.276
1220.723
1230.87
1240.0659
1250.909
1260.187
1270.606
1280.00727
1290.325
130.0106
1300.788
1310.495
1320.735
1330.0565
1340.592
1350.837
1360.423
1370.56
1380.425
1390.247
140.802
1400.00168
1410.145
1420.0932
1430.29
1440.611
1450.0448
1460.993
1470.676
1480.85
1490.597
150.228
1500.0933
1510.635
1520.845
1530.0993
1540.147
1550.787
1560.598
1570.973
1580.924
1590.018
1600.0536
1610.694
1620.918
1630.581
1640.0896
1650.95
1660.952
1670.0509
1680.856
1690.0191
170.0903
180.244
190.0503
20.924
200.293
210.951
220.282
230.163
240.96
250.891
267.86695e-4
270.715
280.618
290.156
30.0182
300.433
310.31
320.0479
330.589
340.483
350.125
360.22
370.103
380.577
390.326
40.639
400.86
410.559
420.19
430.0307
440.0788
450.643
460.033
470.48
480.34
490.0456
50.0848
500.686
510.416
520.656
530.465
540.445
550.957
560.319
570.174
580.698
590.233
60.697
600.155
610.171
620.297
630.236
640.495
650.39
660.298
670.866
680.0339
690.578
70.25
700.167
710.0274
720.98
730.443
740.501
750.0316
760.265
770.396
780.041
790.49
80.0256
800.789
810.759
820.105
830.88
840.437
850.0301
860.244
870.0261
880.593
890.508
90.632
900.0249
910.0273
920.0439
930.94
940.252
950.858
960.154
970.209
980.365
990.266



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: CNhs11101


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)
0000312 (mouse neonate N6 sample)
0011403 (mouse liver- neonate N06 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:684-20A8&oldid=3271680"