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{{f5samples
{{f5samples
|id=FF:1340-24B8
|id=FF:1340-24B8
|name=stomach, neonate N03, biol_rep1
|name=stomach, neonate N03
|sample_id=1340
|sample_id=1340
|rna_tube_id=1340-24B8
|rna_tube_id=24B8
|rna_box=1340-24B8
|rna_box=24
|rna_position=1340-24B8
|rna_position=B8
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
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|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs11193,LSID746,,COMPLETED
|profile_hcage=CNhs11193,LSID746,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:54, 27 February 2012


Name:stomach, neonate N03
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuestomach
dev stage3 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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs11193

00
10
100
1000
10000.234
10010.14
10020.444
10030.174
10040
10050.0549
10060.00158
1007-0.00206
10080
10090.267
101-0.0069
10100
10110
10120
10130.16
10140.432
1015-0.00299
10160.0354
10170.371
10180.289
10190.104
1020
10200
10210.00626
10220.148
10230
10240.0577
10250.797
10260
10270.0427
10280
10290.401
1030.318
10300
10310.338
10320.169
10330.0238
10340.296
10350.0285
10360.0214
10370
10380.0588
10390.0124
1040
10400.162
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 no result for this sample


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: CNhs11193

Jaspar motifP-value
MA0002.20.13
MA0003.10.266
MA0004.10.158
MA0006.10.0422
MA0007.10.682
MA0009.10.158
MA0014.10.967
MA0017.10.339
MA0018.29.35163e-6
MA0019.10.301
MA0024.10.449
MA0025.10.00658
MA0027.10.0592
MA0028.11.83924e-4
MA0029.10.781
MA0030.10.197
MA0031.10.935
MA0035.20.86
MA0038.10.863
MA0039.20.00219
MA0040.10.604
MA0041.10.191
MA0042.10.287
MA0043.12.68106e-4
MA0046.11.17261e-16
MA0047.21.07733e-6
MA0048.10.747
MA0050.10.212
MA0051.10.0227
MA0052.10.00912
MA0055.10.409
MA0057.10.0433
MA0058.10.0121
MA0059.10.142
MA0060.10.0263
MA0061.10.727
MA0062.24.93369e-11
MA0065.20.0821
MA0066.10.171
MA0067.10.157
MA0068.10.0398
MA0069.10.0234
MA0070.10.872
MA0071.10.0482
MA0072.10.25
MA0073.10.653
MA0074.10.779
MA0076.19.41325e-6
MA0077.10.182
MA0078.10.284
MA0079.20.146
MA0080.27.40013e-4
MA0081.16.50169e-5
MA0083.17.38539e-8
MA0084.10.91
MA0087.10.104
MA0088.10.391
MA0090.10.0125
MA0091.10.439
MA0092.10.0555
MA0093.10.0894
MA0099.27.86986e-6
MA0100.10.00385
MA0101.10.157
MA0102.20.812
MA0103.12.06468e-4
MA0104.20.0513
MA0105.10.426
MA0106.10.0165
MA0107.10.336
MA0108.29.1602e-7
MA0111.10.857
MA0112.20.0053
MA0113.10.525
MA0114.10.0184
MA0115.10.413
MA0116.10.227
MA0117.10.252
MA0119.10.0744
MA0122.10.0407
MA0124.10.745
MA0125.10.47
MA0131.10.288
MA0135.10.554
MA0136.11.74657e-7
MA0137.20.82
MA0138.20.502
MA0139.10.376
MA0140.10.712
MA0141.10.195
MA0142.10.125
MA0143.10.69
MA0144.10.242
MA0145.10.00513
MA0146.10.389
MA0147.10.0313
MA0148.17.88988e-8
MA0149.10.767
MA0150.10.687
MA0152.10.155
MA0153.12.97328e-11
MA0154.10.0427
MA0155.10.384
MA0156.16.96984e-6
MA0157.10.742
MA0159.10.892
MA0160.10.0407
MA0162.10.276
MA0163.10.075
MA0164.10.978
MA0258.10.423
MA0259.10.0861



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: CNhs11193

Novel motifP-value
10.478
100.539
1000.768
1010.907
1020.692
1030.0568
1040.929
1050.867
1060.00269
1070.0074
1080.674
1090.202
110.876
1100.513
1110.596
1120.278
1130.473
1140.448
1150.891
1160.449
1170.519
1180.233
1190.156
120.614
1200.739
1210.543
1220.207
1230.429
1240.745
1250.819
1260.114
1270.737
1280.00861
1290.906
130.027
1300.329
1310.813
1320.343
1330.0555
1340.788
1350.894
1360.783
1370.292
1380.00724
1390.372
140.756
1400.0354
1410.823
1420.32
1430.0944
1440.247
1450.118
1460.135
1470.488
1480.892
1490.221
150.875
1500.427
1510.71
1520.031
1530.607
1540.856
1550.89
1565.72562e-8
1570.311
1580.464
1590.0806
1600.0825
1610.492
1620.268
1630.8
1640.481
1650.605
1660.11
1670.448
1680.266
1690.00854
170.0336
180.88
190.0255
20.174
200.266
210.924
220.241
230.283
240.475
250.373
260.00647
270.763
280.863
290.912
30.616
300.149
310.683
320.0357
330.989
340.97
350.445
360.309
370.142
380.787
390.0959
40.0683
400.869
410.213
420.58
430.169
440.777
450.355
460.315
470.562
480.885
490.342
50.288
500.574
510.411
520.0199
530.326
540.223
550.694
560.369
570.503
580.718
590.441
60.193
600.036
610.303
620.949
630.277
640.982
650.668
660.624
670.843
680.146
690.428
70.219
700.628
710.0742
720.928
730.203
740.297
750.87
760.102
770.00446
780.279
790.877
80.586
800.0592
810.874
820.353
830.527
840.941
850.23
860.583
870.354
880.151
890.381
90.181
900.909
910.528
920.19
930.399
940.533
950.673
960.7
970.243
980.934
990.0507



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: CNhs11193


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

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
NA

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