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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008854
|DRA_sample_Accession=CAGE@SAMD00005002
|accession_numbers=CAGE;DRX008991;DRR009865;DRZ001290;DRZ002673
|accession_numbers=CAGE;DRX008991;DRR009865;DRZ001290;DRZ002673
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409

Revision as of 21:50, 31 July 2014


Name:intestine, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11010
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage13 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  SAMD00005002
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11010 CAGE DRX008991 DRR009865
Accession ID Mm9

Library idBAMCTSS
CNhs11010 DRZ001290 DRZ002673
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

CNhs11010

00
10
100
1000
10000
10010.0926
10020.773
1003-0.109
10040
1005-0.0389
1006-0.0304
10070.0992
10080
10090.0395
1010.129
10100
1011-0.0556
10120.0907
1013-0.234
10140.627
10150.226
10160.142
10170
10180
10190
1020
10200
10210.0907
1022-0.0333
10230
10240.0436
10250.833
10260
10270.00132
10280
10290.357
1030.146
10300
10310.367
1032-0.184
10330.0907
10340.0209
10350.0467
10360.225
10370
10380.0595
1039-0.22
1040
10400.109
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: CNhs11010

Jaspar motifP-value
MA0002.26.49357e-4
MA0003.10.0437
MA0004.10.909
MA0006.10.256
MA0007.10.399
MA0009.10.592
MA0014.10.276
MA0017.10.00381
MA0018.20.186
MA0019.10.884
MA0024.11.26653e-6
MA0025.16.76391e-5
MA0027.10.0182
MA0028.10.698
MA0029.10.439
MA0030.10.364
MA0031.10.0539
MA0035.20.435
MA0038.10.239
MA0039.20.00227
MA0040.10.654
MA0041.10.186
MA0042.10.385
MA0043.10.709
MA0046.10.739
MA0047.20.251
MA0048.10.0253
MA0050.10.00192
MA0051.11.42095e-4
MA0052.18.08567e-8
MA0055.10.027
MA0057.10.0817
MA0058.10.96
MA0059.10.468
MA0060.11.95836e-6
MA0061.10.171
MA0062.20.327
MA0065.29.24534e-6
MA0066.10.225
MA0067.10.275
MA0068.10.532
MA0069.10.554
MA0070.10.94
MA0071.10.0447
MA0072.10.0238
MA0073.10.584
MA0074.10.716
MA0076.10.856
MA0077.10.845
MA0078.10.939
MA0079.20.0198
MA0080.22.52132e-11
MA0081.10.118
MA0083.10.0111
MA0084.10.597
MA0087.10.267
MA0088.10.718
MA0090.10.864
MA0091.10.749
MA0092.10.833
MA0093.10.924
MA0099.21.93002e-6
MA0100.10.882
MA0101.10.287
MA0102.20.465
MA0103.10.00524
MA0104.20.374
MA0105.10.703
MA0106.10.506
MA0107.10.0881
MA0108.20.0535
MA0111.10.643
MA0112.20.00184
MA0113.10.648
MA0114.10.00583
MA0115.10.304
MA0116.10.307
MA0117.10.0242
MA0119.10.0408
MA0122.10.197
MA0124.10.405
MA0125.10.76
MA0131.10.305
MA0135.10.111
MA0136.13.26584e-8
MA0137.20.0961
MA0138.21.8949e-4
MA0139.10.286
MA0140.10.574
MA0141.10.00153
MA0142.10.768
MA0143.10.12
MA0144.10.186
MA0145.10.00536
MA0146.10.131
MA0147.10.344
MA0148.10.263
MA0149.10.127
MA0150.16.29089e-4
MA0152.10.00838
MA0153.10.628
MA0154.10.0359
MA0155.10.96
MA0156.15.45826e-4
MA0157.10.0728
MA0159.10.0353
MA0160.10.00213
MA0162.10.933
MA0163.10.849
MA0164.10.541
MA0258.18.36757e-4
MA0259.10.282



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: CNhs11010

Novel motifP-value
10.216
100.734
1000.724
1010.474
1020.564
1030.24
1040.906
1050.296
1060.0467
1070.187
1080.823
1090.0854
110.204
1100.547
1110.17
1120.323
1130.457
1140.00723
1150.683
1160.425
1170.858
1180.939
1190.0497
120.786
1200.508
1210.582
1220.61
1230.262
1240.452
1250.995
1260.963
1270.253
1280.0808
1290.104
130.829
1300.374
1310.0594
1320.973
1330.329
1340.897
1350.686
1360.232
1370.84
1380.299
1390.0807
140.259
1400.166
1410.539
1420.911
1430.669
1440.554
1450.898
1460.312
1470.385
1480.66
1490.344
150.0637
1500.383
1510.0881
1520.0229
1530.635
1540.964
1550.619
1564.62317e-10
1570.792
1580.763
1590.0681
1600.487
1610.961
1620.692
1630.14
1640.526
1650.0786
1660.231
1670.138
1680.62
1690.0172
170.15
180.377
190.673
20.371
200.497
210.462
220.204
230.0801
240.0799
250.168
260.922
270.218
280.204
290.961
30.497
300.464
310.282
320.451
330.796
340.594
350.497
360.789
370.0591
380.246
390.977
40.799
400.43
410.107
420.767
430.251
440.0172
450.295
460.439
470.253
480.154
490.239
50.357
500.952
510.607
520.529
530.53
540.51
550.461
560.292
570.954
580.323
590.0378
60.689
600.212
610.943
620.0602
630.126
640.577
650.0893
660.794
670.871
680.349
690.345
70.298
701.95049e-4
710.671
720.274
730.0124
740.849
750.192
760.336
770.192
780.231
790.552
80.292
800.0468
810.365
820.108
830.304
840.512
850.0195
860.218
870.00134
880.698
890.112
90.476
900.257
910.441
920.319
930.989
940.86
950.0334
960.466
970.708
980.233
990.892



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: CNhs11010


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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
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)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

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)
0000293 (mouse embryonic day 13 sample)
0011330 (mouse intestine- embryo E13 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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