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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000945,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0000062,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0010039,UBERON:0003104,UBERON:0000925,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0005409,UBERON:0007026,UBERON:0001041,UBERON:0009142,UBERON:0006595,UBERON:0006603
|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=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000310,FF:0011494
|comment=
|comment=
|created_by=
|created_by=

Revision as of 00:24, 5 July 2012


Name:stomach, neonate N30
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 stage30 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]


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

CNhs11134

00
10
100
1000
10000.0859
10010.0905
10020.00605
1003-0.0798
10040
10050.25
10060
10070.0383
10080
10090.0207
101-0.13
10100
1011-0.108
10120.0835
10130.199
1014-0.0874
1015-0.376
1016-0.191
10170
10180.586
10190
1020
10200
1021-0.0231
10220.111
10230
10240
10250.686
10260
10270
10280
10290.375
1030.12
10300
1031-0.185
10320.67
10330
10340.131
10350.0624
1036-0.139
10370
10380.0428
10390.16
1040.983
1040-0.0865
10410.1



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: CNhs11134

Jaspar motifP-value
MA0002.20.643
MA0003.10.226
MA0004.10.443
MA0006.10.0373
MA0007.10.939
MA0009.10.121
MA0014.10.319
MA0017.14.28203e-10
MA0018.20.155
MA0019.10.642
MA0024.15.5036e-4
MA0025.10.519
MA0027.10.493
MA0028.10.618
MA0029.10.614
MA0030.10.425
MA0031.10.0265
MA0035.20.76
MA0038.10.912
MA0039.27.88581e-5
MA0040.10.0211
MA0041.10.357
MA0042.10.665
MA0043.10.921
MA0046.13.29615e-27
MA0047.25.95022e-5
MA0048.10.999
MA0050.17.70974e-4
MA0051.17.03903e-4
MA0052.10.00583
MA0055.10.35
MA0057.10.14
MA0058.10.33
MA0059.10.0996
MA0060.10.0497
MA0061.10.454
MA0062.20.742
MA0065.22.29829e-9
MA0066.10.568
MA0067.10.316
MA0068.10.814
MA0069.10.663
MA0070.10.211
MA0071.10.447
MA0072.10.949
MA0073.10.617
MA0074.10.526
MA0076.10.413
MA0077.10.395
MA0078.10.223
MA0079.20.918
MA0080.29.7886e-4
MA0081.10.244
MA0083.10.0227
MA0084.10.0774
MA0087.10.563
MA0088.10.993
MA0090.10.27
MA0091.10.707
MA0092.10.93
MA0093.10.469
MA0099.22.92515e-4
MA0100.10.159
MA0101.10.957
MA0102.20.198
MA0103.11.1132e-5
MA0104.20.0196
MA0105.10.775
MA0106.10.166
MA0107.10.735
MA0108.20.534
MA0111.10.557
MA0112.22.98904e-4
MA0113.10.267
MA0114.11.69505e-18
MA0115.11.00757e-4
MA0116.10.501
MA0117.10.865
MA0119.10.00698
MA0122.10.77
MA0124.10.339
MA0125.10.307
MA0131.10.538
MA0135.10.0922
MA0136.10.0012
MA0137.20.819
MA0138.20.295
MA0139.10.098
MA0140.10.122
MA0141.10.0343
MA0142.10.103
MA0143.10.0229
MA0144.10.257
MA0145.10.00228
MA0146.10.486
MA0147.10.022
MA0148.11.83387e-5
MA0149.10.0401
MA0150.10.198
MA0152.10.192
MA0153.15.1708e-18
MA0154.10.124
MA0155.10.97
MA0156.10.0111
MA0157.10.0223
MA0159.10.0244
MA0160.10.12
MA0162.10.59
MA0163.10.683
MA0164.10.803
MA0258.10.0554
MA0259.10.0584



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: CNhs11134

Novel motifP-value
10.357
100.427
1000.695
1010.993
1020.949
1030.793
1040.683
1050.167
1060.00629
1070.0549
1080.866
1090.072
110.49
1100.331
1110.686
1120.117
1130.455
1140.267
1150.731
1160.657
1170.728
1180.962
1190.136
120.493
1200.869
1210.399
1220.403
1230.331
1240.707
1250.494
1260.0248
1270.553
1280.0207
1290.423
132.39791e-4
1300.849
1310.00148
1320.609
1330.928
1340.549
1350.399
1360.219
1370.4
1380.301
1390.144
140.468
1400.01
1410.322
1420.495
1430.137
1440.287
1450.0925
1460.236
1470.214
1480.199
1490.528
150.172
1500.4
1510.396
1520.0186
1530.61
1540.399
1550.602
1560.0464
1570.791
1580.667
1590.753
1600.305
1610.53
1620.931
1630.706
1640.202
1650.93
1660.284
1670.773
1680.899
1690.0222
170.0218
180.0706
190.0382
20.407
200.976
210.818
220.348
230.35
240.337
250.831
260.0284
270.941
280.498
290.587
30.467
300.4
310.779
320.318
330.242
340.66
350.665
360.805
370.0225
380.282
390.217
40.394
400.534
410.85
420.988
430.349
440.997
450.339
460.441
470.651
480.562
490.26
50.556
500.267
510.621
520.0324
530.915
540.397
550.267
560.386
570.855
580.324
590.875
60.366
600.0206
610.0889
620.56
630.173
640.777
650.0908
660.614
670.0504
680.209
690.482
70.099
700.089
710.357
720.645
730.0603
740.642
750.22
760.63
770.135
780.0412
790.963
80.516
800.721
810.743
820.32
830.0721
840.365
850.062
860.223
870.746
880.831
890.218
90.76
900.529
910.663
920.509
930.385
940.621
950.165
960.948
970.619
980.537
990.103



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: CNhs11134


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)
0000310 (mouse neonate N30 sample)
0011494 (mouse stomach- neonate N30 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
NA

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