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|library_id=CNhs11138
|library_id=CNhs11138
|library_id_phase_based=1:CNhs11138
|name=pancreas, neonate N01
|name=pancreas, neonate N01
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:14, 18 June 2014


Name:pancreas, neonate N01
Species:Mouse (Mus musculus)
Library ID:CNhs11138
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepancreas
dev stage1 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  DRS008924
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11138 CAGE DRX009061 DRR009935
Accession ID Mm9

Library idBAMCTSS
CNhs11138 DRZ001360 DRZ002743
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

CNhs11138

00
10
100
1000
10000
10010.0187
1002-0.00154
10033.496738e-4
10040
10050
1006-0.00402
10070.0926
10080
10090.12
1010.0501
10100.39
10115.634715e-4
10120
10130.306
10140.39
10150.0957
1016-0.0484
10170
10180
10190
1020
10200
10210
10220.331
10230
10240.137
10250.135
10260.135
10270
10280
1029-0.013
1030.242
10300
10310.241
10320.0679
10330.0561
10340.39
10350.135
10360.113
10370
10380.0265
10390.0218
1040
10400.0217
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: CNhs11138

Jaspar motifP-value
MA0002.20.0181
MA0003.10.384
MA0004.10.516
MA0006.10.039
MA0007.10.522
MA0009.10.291
MA0014.10.812
MA0017.10.604
MA0018.22.7005e-6
MA0019.10.537
MA0024.17.79718e-4
MA0025.10.48
MA0027.10.594
MA0028.10.478
MA0029.10.924
MA0030.10.917
MA0031.10.779
MA0035.20.753
MA0038.10.916
MA0039.20.0814
MA0040.10.635
MA0041.10.397
MA0042.10.659
MA0043.10.0291
MA0046.12.71062e-16
MA0047.20.00664
MA0048.10.307
MA0050.10.352
MA0051.10.818
MA0052.18.45454e-8
MA0055.10.424
MA0057.10.76
MA0058.10.722
MA0059.10.0217
MA0060.10.889
MA0061.10.989
MA0062.20.176
MA0065.20.405
MA0066.10.495
MA0067.10.0327
MA0068.10.0784
MA0069.10.503
MA0070.10.837
MA0071.10.741
MA0072.10.887
MA0073.10.849
MA0074.10.0374
MA0076.10.119
MA0077.10.846
MA0078.10.706
MA0079.20.53
MA0080.20.135
MA0081.10.403
MA0083.10.0283
MA0084.10.289
MA0087.10.53
MA0088.10.338
MA0090.10.153
MA0091.12.86777e-4
MA0092.10.35
MA0093.10.596
MA0099.20.00182
MA0100.10.0063
MA0101.10.936
MA0102.20.0321
MA0103.15.07519e-5
MA0104.20.898
MA0105.10.705
MA0106.10.309
MA0107.10.64
MA0108.20.014
MA0111.10.75
MA0112.20.0623
MA0113.10.572
MA0114.10.153
MA0115.10.531
MA0116.10.535
MA0117.10.121
MA0119.10.401
MA0122.10.439
MA0124.10.651
MA0125.10.104
MA0131.10.367
MA0135.10.999
MA0136.10.0105
MA0137.20.0522
MA0138.20.0423
MA0139.10.554
MA0140.10.412
MA0141.10.947
MA0142.10.974
MA0143.10.924
MA0144.10.0536
MA0145.10.127
MA0146.10.563
MA0147.10.292
MA0148.10.00179
MA0149.10.116
MA0150.10.0285
MA0152.10.231
MA0153.13.71077e-7
MA0154.10.0619
MA0155.10.105
MA0156.10.263
MA0157.10.642
MA0159.10.726
MA0160.10.244
MA0162.10.771
MA0163.10.0753
MA0164.10.434
MA0258.10.437
MA0259.10.938



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: CNhs11138

Novel motifP-value
10.563
100.558
1000.675
1010.395
1020.726
1030.296
1040.781
1050.556
1060.0309
1070.657
1080.385
1090.09
110.618
1100.118
1110.973
1120.317
1130.0307
1140.104
1150.531
1160.902
1170.475
1180.601
1190.473
120.048
1200.438
1210.0512
1220.592
1230.597
1240.352
1250.806
1260.0637
1270.522
1280.225
1290.433
136.38317e-4
1300.191
1310.441
1320.806
1330.148
1340.275
1350.642
1360.0507
1370.124
1380.00661
1390.825
140.918
1400.0503
1410.233
1420.378
1430.646
1440.304
1450.172
1460.993
1470.216
1480.0255
1490.365
150.786
1500.375
1510.539
1520.00482
1530.317
1540.672
1550.765
1560.00384
1570.239
1580.829
1590.87
1600.149
1610.399
1620.4
1630.671
1640.361
1650.578
1660.354
1670.702
1680.842
1690.0534
170.403
180.142
190.0195
20.68
200.745
210.544
220.529
230.898
240.133
250.333
260.00159
270.951
280.161
290.688
30.892
300.718
310.59
320.149
330.47
340.867
350.257
360.535
370.149
380.784
390.0566
40.356
400.919
410.0454
420.511
430.513
440.705
450.795
460.42
470.831
480.887
490.619
50.727
500.26
510.908
520.261
530.804
540.589
550.94
560.508
570.918
580.624
590.335
60.995
600.313
610.221
620.61
630.405
640.913
650.348
660.447
670.718
680.754
690.839
70.205
700.908
710.0623
720.733
730.0784
740.291
750.741
760.887
770.238
780.24
790.0462
80.169
800.278
810.54
820.597
830.816
840.0061
850.835
860.397
870.28
880.364
890.746
90.67
900.706
910.211
920.592
930.296
940.26
950.889
960.308
970.0574
980.727
990.261



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: CNhs11138


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)
0011251 (mouse pancreas- neonate N01 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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