Personal tools

FF:657-19C2: 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@SAMD00004943
|DRA_sample_Accession=CAGE@SAMD00004943
|accession_numbers=CAGE;DRX009151;DRR010025;DRZ001450;DRZ002833
|accession_numbers=CAGE;DRX009151;DRR010025;DRZ001450;DRZ002833;DRZ012800;DRZ014183
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:42, 10 August 2017


Name:whole body, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs10525
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage0 day neonate
sexfemale
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  SAMD00004943
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10525 CAGE DRX009151 DRR010025
Accession ID Mm9

Library idBAMCTSS
CNhs10525 DRZ001450 DRZ002833
Accession ID Mm10

Library idBAMCTSS
CNhs10525 DRZ012800 DRZ014183
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

CNhs10525

00
10.129
100
1000.0845
10000.206
10010.0695
1002-0.00451
10030.0873
10040
10050.022
10060.237
1007-0.00118
10080
10090.17
101-0.016
10100
10110.0845
10120
1013-0.0543
10140.23
1015-0.0624
10160.222
10170.0845
10180.0845
10190
1020
10200
10210
10220.406
10230
10240.311
10250.585
10260.126
10270.107
10280
1029-0.0207
1030.573
10300
10310.361
10320.0108
10330
10340.155
10350.0845
1036-0.00681
10370
10380.0206
10390.0904
1040
10400.252
10410.155



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: CNhs10525

Jaspar motifP-value
MA0002.20.679
MA0003.10.0265
MA0004.10.153
MA0006.10.215
MA0007.10.211
MA0009.10.519
MA0014.10.213
MA0017.10.13
MA0018.28.60808e-4
MA0019.10.763
MA0024.10.0282
MA0025.10.456
MA0027.10.206
MA0028.11.57843e-8
MA0029.10.292
MA0030.10.00827
MA0031.10.245
MA0035.20.0744
MA0038.10.144
MA0039.20.308
MA0040.10.212
MA0041.10.281
MA0042.10.415
MA0043.10.0142
MA0046.13.34964e-26
MA0047.20.0533
MA0048.10.00158
MA0050.10.0793
MA0051.10.0822
MA0052.12.60886e-19
MA0055.11.03463e-5
MA0057.10.488
MA0058.10.0293
MA0059.10.00348
MA0060.10.0795
MA0061.10.717
MA0062.23.43294e-14
MA0065.20.0915
MA0066.10.84
MA0067.10.191
MA0068.10.882
MA0069.10.431
MA0070.10.191
MA0071.10.287
MA0072.10.793
MA0073.10.924
MA0074.10.949
MA0076.11.35763e-9
MA0077.10.718
MA0078.10.0489
MA0079.20.0148
MA0080.24.95348e-5
MA0081.10.0389
MA0083.12.20393e-8
MA0084.10.887
MA0087.10.122
MA0088.10.0716
MA0090.10.0473
MA0091.10.353
MA0092.10.0727
MA0093.10.113
MA0099.20.116
MA0100.10.0155
MA0101.10.0903
MA0102.20.325
MA0103.10.541
MA0104.20.0379
MA0105.10.77
MA0106.10.308
MA0107.10.303
MA0108.22.33065e-57
MA0111.10.93
MA0112.20.334
MA0113.10.483
MA0114.10.0316
MA0115.10.817
MA0116.10.793
MA0117.10.562
MA0119.10.262
MA0122.10.571
MA0124.10.853
MA0125.10.00939
MA0131.10.193
MA0135.10.0196
MA0136.16.19661e-13
MA0137.20.00438
MA0138.27.81506e-7
MA0139.10.406
MA0140.10.136
MA0141.10.42
MA0142.10.447
MA0143.10.753
MA0144.10.356
MA0145.10.015
MA0146.10.609
MA0147.10.0255
MA0148.10.00893
MA0149.10.00875
MA0150.10.583
MA0152.10.99
MA0153.19.36347e-12
MA0154.10.156
MA0155.10.048
MA0156.13.20817e-11
MA0157.10.174
MA0159.10.244
MA0160.10.593
MA0162.10.712
MA0163.10.999
MA0164.10.297
MA0258.10.699
MA0259.10.0706



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: CNhs10525

Novel motifP-value
10.671
100.114
1000.67
1010.164
1020.2
1030.18
1040.792
1050.541
1060.053
1070.012
1080.376
1090.709
110.658
1100.456
1110.0454
1120.614
1130.469
1140.895
1150.813
1160.103
1170.0112
1180.402
1190.593
120.653
1200.788
1210.651
1220.281
1230.194
1240.454
1250.101
1260.163
1270.768
1280.152
1290.804
130.135
1300.664
1310.181
1320.555
1330.151
1340.237
1350.398
1360.736
1370.875
1380.81
1390.968
140.293
1400.775
1410.593
1420.337
1430.201
1440.842
1450.586
1460.21
1470.74
1480.8
1490.332
150.188
1500.915
1510.529
1520.1
1530.323
1540.479
1550.0855
1560.856
1570.0483
1580.00651
1590.0974
1600.307
1610.0632
1620.222
1630.692
1640.123
1650.781
1660.166
1670.0118
1680.0031
1690.172
170.489
180.549
190.257
20.0135
200.00823
210.185
220.519
230.133
240.292
250.642
260.691
270.309
280.962
290.0402
30.637
300.0996
310.473
320.0932
330.395
340.218
350.393
360.0684
370.821
380.972
390.669
40.658
400.473
410.359
420.696
430.634
440.652
450.135
460.867
470.979
480.782
490.855
50.94
500.522
510.649
520.0797
530.242
540.333
550.66
560.405
570.301
580.942
590.063
60.65
600.236
610.314
620.942
630.488
640.897
650.557
660.493
670.443
680.562
690.814
70.961
700.279
710.653
720.853
730.881
740.845
750.12
760.00774
770.146
780.519
790.925
80.743
800.554
810.332
820.622
830.885
840.181
850.261
860.629
870.351
880.308
890.302
90.294
900.0187
910.539
920.369
930.0464
940.432
950.237
960.878
970.7
980.836
990.133



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: CNhs10525


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)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011398 (mouse whole body- neonate N00 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
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:657-19C2&oldid=4345903"