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|library_id=CNhs11105
 
|library_id=CNhs11105
 
|library_id_phase_based=2:CNhs11105
 
|library_id_phase_based=2:CNhs11105
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;645
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;645
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N00.CNhs11105.645-26G9.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N00.CNhs11105.645-26G9.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N00.CNhs11105.645-26G9.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N00.CNhs11105.645-26G9.mm10.nobarcode.ctss.bed.gz

Revision as of 13:35, 18 May 2017


Name:pancreas, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11105
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepancreas
dev stage0 day 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  SAMD00005164
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11105 CAGE DRX009060 DRR009934
Accession ID Mm9

Library idBAMCTSS
CNhs11105 DRZ001359 DRZ002742
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

CNhs11105

00
10
100
1000
10000.0272
1001-0.0596
10020.0484
1003-0.0457
10040
10050
1006-0.0453
10070.098
10080
10090.16
1010.0366
10100.249
1011-0.0837
10120
10130.213
10140.319
1015-0.0489
10160.0881
10170
10180.133
10190
1020
10200
10210
10220.172
10230
10240
10250.426
10260
10270
10280
10290.0821
1030.181
10300
10310.178
10320.132
10330
10340.33
10350
10360.0406
10370
10380.0786
10390.0288
1040
10400.163
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: CNhs11105

Jaspar motifP-value
MA0002.20.755
MA0003.10.205
MA0004.10.733
MA0006.10.0197
MA0007.10.138
MA0009.10.974
MA0014.10.736
MA0017.19.21128e-16
MA0018.20.00892
MA0019.10.227
MA0024.10.00845
MA0025.10.417
MA0027.10.336
MA0028.10.0447
MA0029.10.489
MA0030.10.251
MA0031.10.16
MA0035.23.68645e-5
MA0038.10.953
MA0039.20.00111
MA0040.10.844
MA0041.10.966
MA0042.10.426
MA0043.10.105
MA0046.13.08617e-64
MA0047.22.82087e-5
MA0048.10.674
MA0050.18.37301e-6
MA0051.10.00206
MA0052.10.00447
MA0055.10.535
MA0057.10.383
MA0058.10.652
MA0059.10.874
MA0060.10.335
MA0061.10.95
MA0062.20.0286
MA0065.23.08493e-5
MA0066.10.897
MA0067.10.494
MA0068.10.196
MA0069.10.0647
MA0070.10.864
MA0071.10.169
MA0072.10.43
MA0073.10.862
MA0074.10.0715
MA0076.10.0467
MA0077.10.559
MA0078.10.419
MA0079.20.0191
MA0080.20.156
MA0081.10.301
MA0083.10.77
MA0084.10.361
MA0087.10.791
MA0088.10.598
MA0090.10.0636
MA0091.10.222
MA0092.10.324
MA0093.10.695
MA0099.20.132
MA0100.14.96694e-4
MA0101.10.684
MA0102.20.477
MA0103.16.9336e-5
MA0104.20.138
MA0105.10.276
MA0106.10.542
MA0107.10.508
MA0108.20.00158
MA0111.10.988
MA0112.20.0984
MA0113.10.691
MA0114.11.03194e-20
MA0115.14.4702e-4
MA0116.10.0606
MA0117.10.768
MA0119.10.487
MA0122.10.801
MA0124.10.552
MA0125.10.552
MA0131.10.716
MA0135.10.0115
MA0136.10.972
MA0137.20.00891
MA0138.20.56
MA0139.10.423
MA0140.10.00254
MA0141.10.154
MA0142.10.119
MA0143.10.263
MA0144.18.92654e-4
MA0145.10.0034
MA0146.10.218
MA0147.10.201
MA0148.11.83212e-7
MA0149.10.169
MA0150.10.981
MA0152.10.537
MA0153.15.1291e-32
MA0154.10.0733
MA0155.10.054
MA0156.10.328
MA0157.10.0761
MA0159.10.67
MA0160.10.194
MA0162.10.676
MA0163.10.237
MA0164.10.224
MA0258.10.579
MA0259.10.247



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: CNhs11105

Novel motifP-value
10.873
100.381
1000.474
1010.533
1020.472
1030.486
1040.707
1050.243
1060.00921
1070.0196
1080.601
1090.225
110.706
1101
1110.344
1120.102
1130.412
1140.9
1150.619
1160.274
1170.447
1180.364
1190.374
120.254
1200.383
1210.506
1220.297
1230.633
1240.229
1250.213
1260.234
1270.958
1280.331
1290.339
130.00187
1300.995
1310.213
1320.511
1330.559
1340.313
1350.548
1360.0033
1370.236
1380.00686
1390.402
140.696
1400.411
1410.389
1420.189
1430.204
1440.733
1450.425
1460.119
1470.291
1480.0315
1490.309
150.945
1500.337
1510.785
1520.00282
1530.535
1540.566
1550.844
1562.80409e-4
1570.042
1580.624
1590.662
1600.219
1610.414
1620.968
1630.208
1640.965
1650.977
1660.496
1670.11
1680.0673
1690.0833
170.224
180.1
190.063
20.0407
200.336
210.73
220.188
230.271
240.38
250.699
260.0714
270.584
280.542
290.33
30.9
300.101
310.533
320.231
330.301
340.513
350.139
360.727
370.0745
380.461
390.15
40.212
400.401
410.11
420.909
430.704
440.72
450.0606
460.844
470.715
480.816
490.834
50.519
500.209
510.981
520.0359
530.538
540.812
550.0522
560.508
570.0702
580.908
590.123
60.905
600.0295
610.602
620.54
630.428
640.854
650.519
660.984
670.358
680.384
690.959
70.121
700.934
710.917
720.933
730.0523
740.517
750.832
760.0955
770.0585
780.386
790.954
80.781
800.603
810.607
820.924
830.731
840.433
850.223
860.427
870.0288
880.452
890.684
90.737
900.597
910.349
920.278
930.921
940.0556
950.518
960.0238
970.0331
980.693
990.256



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: CNhs11105


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)
0001264 (pancreas)
0002100 (trunk)
0000479 (tissue)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002323 (body cavity)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0000949 (endocrine system)

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)
0011266 (mouse pancreas- 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)