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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008958
|DRA_sample_Accession=CAGE@SAMD00005926
|accession_numbers=CAGE;DRX009095;DRR009969;DRZ001394;DRZ002777
|accession_numbers=CAGE;DRX009095;DRR009969;DRZ001394;DRZ002777
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,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:0000922,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

Revision as of 21:29, 31 July 2014


Name:stomach, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs10999
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuestomach
dev stage18 days embryo
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  SAMD00005926
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10999 CAGE DRX009095 DRR009969
Accession ID Mm9

Library idBAMCTSS
CNhs10999 DRZ001394 DRZ002777
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

CNhs10999

00
10
100
1000
10000.122
10010.0822
10020.428
10030.0939
10040
10050.197
1006-0.0659
1007-0.0227
10080
10090.121
1010.00106
10100
10110
10120
10130.0443
10140.538
1015-0.00708
10160.0847
10170.852
10180.631
10190
1020
10200
10210
10220.0154
10230
10240.0565
10250.757
10260.0563
10270
10280
10290.304
1030.273
10300
10310.349
10320.219
10330
10340
10350
10360.0466
10370
10380.0126
1039-0.0106
1040
10400.0979
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: CNhs10999

Jaspar motifP-value
MA0002.20.415
MA0003.10.285
MA0004.10.304
MA0006.10.0852
MA0007.10.778
MA0009.10.0502
MA0014.10.757
MA0017.10.063
MA0018.22.66634e-5
MA0019.10.623
MA0024.10.23
MA0025.19.49205e-4
MA0027.10.0179
MA0028.10.00178
MA0029.10.915
MA0030.10.289
MA0031.10.718
MA0035.20.168
MA0038.10.589
MA0039.20.00315
MA0040.10.587
MA0041.10.127
MA0042.10.193
MA0043.13.14172e-4
MA0046.14.18051e-24
MA0047.21.65062e-6
MA0048.10.585
MA0050.10.467
MA0051.10.033
MA0052.10.00366
MA0055.10.373
MA0057.10.0668
MA0058.10.114
MA0059.10.444
MA0060.10.0846
MA0061.10.829
MA0062.22.16164e-8
MA0065.20.086
MA0066.10.166
MA0067.10.159
MA0068.10.0671
MA0069.10.0434
MA0070.10.494
MA0071.10.0529
MA0072.10.323
MA0073.10.606
MA0074.10.963
MA0076.11.61676e-4
MA0077.10.306
MA0078.10.233
MA0079.20.475
MA0080.20.0317
MA0081.10.00121
MA0083.11.50976e-5
MA0084.10.945
MA0087.10.298
MA0088.10.178
MA0090.10.0801
MA0091.10.679
MA0092.10.213
MA0093.10.261
MA0099.22.81008e-5
MA0100.10.00702
MA0101.10.343
MA0102.20.769
MA0103.15.42171e-5
MA0104.20.181
MA0105.10.0674
MA0106.10.0927
MA0107.10.379
MA0108.21.44913e-7
MA0111.10.855
MA0112.20.00455
MA0113.10.509
MA0114.10.00241
MA0115.10.976
MA0116.10.0415
MA0117.10.194
MA0119.10.0986
MA0122.10.182
MA0124.10.997
MA0125.10.576
MA0131.10.238
MA0135.10.355
MA0136.17.20797e-5
MA0137.20.737
MA0138.20.745
MA0139.10.25
MA0140.10.318
MA0141.10.361
MA0142.10.0504
MA0143.10.138
MA0144.10.185
MA0145.10.00923
MA0146.10.655
MA0147.10.153
MA0148.12.06192e-7
MA0149.10.491
MA0150.10.602
MA0152.10.728
MA0153.11.20894e-16
MA0154.10.00876
MA0155.10.275
MA0156.10.0023
MA0157.10.321
MA0159.10.89
MA0160.10.194
MA0162.10.255
MA0163.10.0139
MA0164.10.834
MA0258.10.17
MA0259.10.177



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: CNhs10999

Novel motifP-value
10.532
100.439
1000.604
1010.717
1020.789
1030.0414
1040.868
1050.779
1060.00757
1070.0151
1080.637
1090.199
110.657
1100.479
1110.505
1120.161
1130.517
1140.995
1150.931
1160.167
1170.617
1180.366
1190.159
120.83
1200.523
1210.454
1220.341
1230.629
1240.768
1250.876
1260.117
1270.569
1280.0188
1290.945
130.0231
1300.461
1310.845
1320.322
1330.77
1340.402
1350.998
1360.807
1370.887
1380.00633
1390.49
140.768
1400.045
1410.369
1420.677
1430.0809
1440.207
1450.0916
1460.346
1470.787
1480.559
1490.213
150.825
1500.456
1510.773
1520.0833
1530.563
1540.868
1550.946
1560.00513
1570.275
1580.807
1590.151
1600.0384
1610.22
1620.256
1630.978
1640.519
1650.784
1660.225
1670.29
1680.0739
1690.025
170.0374
180.685
190.0316
20.244
200.24
210.274
220.215
230.134
240.615
250.358
260.0161
270.693
280.879
290.921
30.57
300.103
310.902
320.0412
330.727
340.72
350.697
360.371
370.193
380.69
390.156
40.198
400.765
410.379
420.659
430.216
440.774
450.266
460.299
470.531
480.762
490.457
50.517
500.526
510.421
520.0431
530.275
540.21
550.961
560.377
570.387
580.626
590.226
60.17
600.0538
610.438
620.759
630.408
640.873
650.365
660.528
670.901
680.0774
690.319
70.246
700.875
710.0785
720.572
730.306
740.517
750.715
760.121
770.00339
780.245
790.915
80.687
800.181
810.592
820.285
830.988
840.897
850.17
860.556
870.484
880.145
890.352
90.265
900.846
910.671
920.113
930.266
940.522
950.656
960.43
970.266
980.871
990.0344



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: CNhs10999


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)
0000922 (embryo)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000302 (mouse embryonic day 18 sample)
0011514 (mouse stomach- embryo E18 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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