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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005361
|DRA_sample_Accession=CAGE@SAMD00005361
|accession_numbers=CAGE;DRX009097;DRR009971;DRZ001396;DRZ002779
|accession_numbers=CAGE;DRX009097;DRR009971;DRZ001396;DRZ002779;DRZ012746;DRZ014129
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000945,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010039,UBERON:0010317,UBERON:0001555,UBERON:0005409,UBERON:0001041
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000945,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010039,UBERON:0010317,UBERON:0001555,UBERON:0005409,UBERON:0001041
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:44, 10 August 2017


Name:stomach, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11210
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuestomach
dev stage7 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  SAMD00005361
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11210 CAGE DRX009097 DRR009971
Accession ID Mm9

Library idBAMCTSS
CNhs11210 DRZ001396 DRZ002779
Accession ID Mm10

Library idBAMCTSS
CNhs11210 DRZ012746 DRZ014129
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

CNhs11210

00
10.0345
100
1000
10000.161
10010.0957
10020.323
10030.11
10040
10050.132
10060.0962
10070.0315
10080
10090.191
101-0.0161
10100.0664
10110.0655
10120.0159
10130.179
10140.175
1015-0.0407
10160.0762
10170.0962
10180.334
10190.0664
1020
10200
10210
10220.281
10230
10240.138
10250.826
10260
10270.0352
10280.0345
10290.235
1030.355
10300
10310.312
10320.188
1033-0.0396
10340.284
10350.0664
1036-0.0588
10370
10380.179
10390.112
1040
10400.147
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: CNhs11210

Jaspar motifP-value
MA0002.20.858
MA0003.10.133
MA0004.10.255
MA0006.10.0543
MA0007.10.924
MA0009.10.412
MA0014.10.963
MA0017.10.00145
MA0018.21.05774e-4
MA0019.10.601
MA0024.10.0431
MA0025.10.398
MA0027.10.0632
MA0028.18.95519e-6
MA0029.10.887
MA0030.15.05533e-4
MA0031.10.0207
MA0035.20.0995
MA0038.10.989
MA0039.20.00317
MA0040.10.597
MA0041.10.461
MA0042.10.267
MA0043.10.00189
MA0046.11.3569e-56
MA0047.21.59747e-12
MA0048.10.47
MA0050.10.0959
MA0051.10.538
MA0052.10.426
MA0055.10.0432
MA0057.10.0843
MA0058.10.0381
MA0059.10.049
MA0060.10.0267
MA0061.10.883
MA0062.28.04541e-11
MA0065.28.90416e-4
MA0066.10.397
MA0067.10.259
MA0068.10.362
MA0069.10.0421
MA0070.10.657
MA0071.10.32
MA0072.10.703
MA0073.10.847
MA0074.10.899
MA0076.12.0303e-6
MA0077.10.27
MA0078.10.153
MA0079.20.021
MA0080.20.107
MA0081.10.00169
MA0083.11.56913e-9
MA0084.10.897
MA0087.10.0756
MA0088.10.479
MA0090.10.011
MA0091.10.209
MA0092.10.0706
MA0093.10.178
MA0099.21.66115e-6
MA0100.10.00319
MA0101.10.375
MA0102.20.613
MA0103.10.00383
MA0104.20.0288
MA0105.10.857
MA0106.10.187
MA0107.10.787
MA0108.22.39243e-9
MA0111.10.929
MA0112.20.0184
MA0113.10.466
MA0114.19.3969e-6
MA0115.10.666
MA0116.10.843
MA0117.10.262
MA0119.10.059
MA0122.10.205
MA0124.10.941
MA0125.10.808
MA0131.10.161
MA0135.10.369
MA0136.19.66533e-5
MA0137.20.879
MA0138.20.0714
MA0139.10.452
MA0140.10.891
MA0141.10.302
MA0142.10.0201
MA0143.10.977
MA0144.10.404
MA0145.10.00107
MA0146.10.421
MA0147.10.0124
MA0148.12.10633e-15
MA0149.10.529
MA0150.10.788
MA0152.10.989
MA0153.14.35342e-31
MA0154.10.0854
MA0155.10.338
MA0156.14.24954e-4
MA0157.10.0136
MA0159.10.925
MA0160.10.343
MA0162.10.615
MA0163.10.69
MA0164.10.847
MA0258.10.32
MA0259.10.0351



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: CNhs11210

Novel motifP-value
10.963
100.395
1000.465
1010.709
1020.327
1030.196
1040.966
1050.381
1060.00101
1070.00124
1080.888
1090.477
110.938
1100.771
1110.947
1120.344
1130.894
1140.555
1150.903
1160.403
1170.102
1180.221
1190.116
120.753
1200.384
1210.962
1220.273
1230.468
1240.617
1250.3
1260.222
1270.991
1280.00419
1290.823
130.0641
1300.223
1310.418
1320.435
1330.335
1340.818
1350.306
1360.456
1370.617
1380.0195
1390.415
140.427
1400.152
1410.69
1420.692
1430.015
1440.221
1450.305
1460.0433
1470.855
1480.742
1490.0974
150.977
1500.379
1510.59
1520.00708
1530.854
1540.865
1550.479
1560.0116
1570.048
1580.227
1590.498
1600.146
1610.838
1620.174
1630.399
1640.799
1650.778
1660.0796
1670.146
1680.0931
1690.00754
170.091
180.546
190.0278
20.0108
200.111
210.396
220.168
230.144
240.283
250.357
260.0386
270.554
280.854
290.326
30.846
300.112
310.548
320.035
330.963
340.623
350.285
360.14
370.344
380.711
390.0978
40.278
400.77
410.16
420.835
430.255
440.735
450.156
460.493
470.762
480.966
490.407
50.497
500.53
510.433
520.0139
530.237
540.247
550.995
560.442
570.837
580.684
590.376
60.53
600.0273
610.412
620.853
630.288
640.752
650.394
660.689
670.594
680.143
690.653
70.521
701
710.494
720.807
730.258
740.747
750.683
760.0273
770.0165
780.273
790.717
80.912
800.561
810.681
820.297
830.995
840.554
850.225
860.565
870.429
880.178
890.236
90.18
900.31
910.748
920.242
930.423
940.163
950.55
960.658
970.155
980.823
990.0386



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: CNhs11210


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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000313 (mouse neonate N7 sample)
0011410 (mouse stomach- neonate N07 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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