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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004720
|DRA_sample_Accession=CAGE@SAMD00004720
|accession_numbers=CAGE;DRX008948;DRR009822;DRZ001247;DRZ002630
|accession_numbers=CAGE;DRX008948;DRR009822;DRZ001247;DRZ002630;DRZ012597;DRZ013980
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001851,UBERON:0005889,UBERON:0000479,UBERON:0000064,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000470
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001851,UBERON:0005889,UBERON:0000479,UBERON:0000064,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000470
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:17, 10 August 2017


Name:cortex, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11107
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecortex
dev stage30 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  SAMD00004720
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11107 CAGE DRX008948 DRR009822
Accession ID Mm9

Library idBAMCTSS
CNhs11107 DRZ001247 DRZ002630
Accession ID Mm10

Library idBAMCTSS
CNhs11107 DRZ012597 DRZ013980
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

CNhs11107

00
10.828
100
1000
10000
10010.0729
1002-0.0956
10030.16
10040
10050.114
10060.696
10070.0595
10080
1009-0.179
101-0.0521
10100
10110.879
10120.512
10130.152
10140
1015-0.0015
1016-0.2
10170
10180
10190
1020
10200
1021-0.0229
1022-0.0251
10230
10240
10250
10260
10270.306
10280
10290.0704
103-0.0788
10300
1031-0.441
10320.129
1033-0.0647
10340
10350
1036-0.249
10370
10380.00542
10390.0996
1040
1040-0.318
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: CNhs11107

Jaspar motifP-value
MA0002.20.00325
MA0003.10.28
MA0004.10.572
MA0006.10.135
MA0007.10.359
MA0009.10.95
MA0014.10.691
MA0017.17.55596e-7
MA0018.20.00908
MA0019.10.25
MA0024.10.0506
MA0025.10.015
MA0027.10.0563
MA0028.10.0897
MA0029.10.922
MA0030.10.773
MA0031.10.185
MA0035.20.0127
MA0038.10.552
MA0039.20.0209
MA0040.10.0876
MA0041.10.765
MA0042.10.414
MA0043.10.149
MA0046.14.35054e-11
MA0047.23.0384e-4
MA0048.10.0571
MA0050.11.61357e-4
MA0051.10.0127
MA0052.10.672
MA0055.10.0162
MA0057.10.507
MA0058.10.448
MA0059.10.169
MA0060.10.488
MA0061.10.0371
MA0062.20.00267
MA0065.21.31542e-6
MA0066.10.0203
MA0067.10.511
MA0068.10.333
MA0069.10.0534
MA0070.10.511
MA0071.10.0283
MA0072.10.331
MA0073.10.726
MA0074.10.104
MA0076.10.219
MA0077.10.716
MA0078.10.66
MA0079.20.453
MA0080.25.42935e-10
MA0081.10.223
MA0083.10.00763
MA0084.10.741
MA0087.10.665
MA0088.10.315
MA0090.10.197
MA0091.10.182
MA0092.10.305
MA0093.10.6
MA0099.20.00745
MA0100.10.337
MA0101.10.0223
MA0102.20.386
MA0103.10.217
MA0104.20.901
MA0105.10.0117
MA0106.10.0693
MA0107.10.0421
MA0108.23.64563e-4
MA0111.10.887
MA0112.27.78892e-4
MA0113.10.297
MA0114.16.94097e-6
MA0115.13.38497e-5
MA0116.10.0685
MA0117.10.891
MA0119.10.112
MA0122.10.897
MA0124.10.544
MA0125.10.0304
MA0131.10.828
MA0135.10.794
MA0136.13.76654e-11
MA0137.20.122
MA0138.20.00167
MA0139.10.475
MA0140.14.02241e-4
MA0141.14.74423e-4
MA0142.10.438
MA0143.10.683
MA0144.10.0992
MA0145.10.12
MA0146.10.02
MA0147.10.774
MA0148.12.14096e-4
MA0149.10.154
MA0150.10.184
MA0152.10.16
MA0153.11.1127e-11
MA0154.10.0481
MA0155.10.347
MA0156.18.91241e-8
MA0157.10.07
MA0159.10.00151
MA0160.10.00324
MA0162.10.151
MA0163.10.00108
MA0164.10.876
MA0258.10.0192
MA0259.10.969



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: CNhs11107

Novel motifP-value
10.23
100.0575
1000.408
1010.849
1020.883
1030.0627
1040.769
1050.618
1060.0497
1070.159
1080.725
1090.00437
110.075
1100.0443
1110.113
1120.0093
1130.392
1140.449
1150.959
1160.252
1170.00402
1180.493
1190.29
120.942
1200.983
1210.427
1220.798
1230.00352
1240.0426
1250.309
1260.0269
1270.422
1280.0477
1290.298
132.07711e-7
1300.0848
1310.507
1320.703
1330.596
1340.0983
1350.421
1360.038
1370.711
1380.858
1390.246
140.94
1400.071
1410.525
1420.814
1430.416
1440.674
1452.64552e-4
1460.316
1470.247
1480.368
1490.468
150.226
1500.0507
1510.849
1520.106
1530.825
1540.983
1550.307
1560.00225
1570.353
1580.207
1590.605
1600.162
1610.0435
1620.581
1630.741
1640.0689
1650.0971
1660.964
1670.585
1680.586
1690.00365
170.0527
180.862
190.0691
20.874
200.0521
210.199
220.134
230.741
240.0322
250.777
265.7437e-7
270.604
280.687
290.0212
30.0455
300.933
310.986
320.503
330.194
340.594
350.805
360.297
370.0239
380.533
390.309
40.193
400.151
410.417
420.163
430.127
440.443
450.662
460.133
470.323
480.253
490.245
50.181
500.24
510.777
520.247
530.493
540.967
550.903
560.418
570.726
580.374
590.101
60.978
600.0388
610.0345
620.255
630.133
640.619
650.408
660.553
670.487
680.553
690.23
70.0207
700.121
710.00588
720.607
730.0332
740.928
750.049
760.568
770.34
780.00232
790.546
80.0627
800.568
810.858
820.229
830.066
840.792
850.176
860.196
870.0529
880.462
890.789
90.442
900.276
910.0984
920.24
930.114
940.895
950.0236
960.47
970.97
980.409
990.411



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: CNhs11107


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)
0001851 (cortex)
0005889 (zygote cortex)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000470 (cell part)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011469 (mouse cortex- neonate N30 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)

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