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{{f5samples
{{f5samples
|id=FF:1345-25G2
|id=FF:1345-25G2
|name=liver, neonate N03, biol_rep1
|name=liver, neonate N03
|sample_id=1345
|sample_id=1345
|rna_tube_id=1345-25G2
|rna_tube_id=25G2
|rna_box=1345-25G2
|rna_box=25
|rna_position=1345-25G2
|rna_position=G2
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs11123,LSID734,,COMPLETED
|profile_hcage=CNhs11123,LSID734,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:41, 27 February 2012


Name:liver, 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
tissueliver
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

CNhs11123

00
10
100
1000
10000
10010.105
10020.00541
10030.0184
10040
10050.105
1006-0.0097
1007-0.11
10080
1009-0.0946
1010.0438
10100
1011-0.147
10120
10130.26
10140.0203
1015-0.156
1016-0.272
10170
10180
10190
1020
10200
10210.0362
10220.137
10230
10240.116
10250.322
10260
10270
10280
10290.199
103-0.0138
10300.105
1031-0.251
1032-0.232
10330
10340.66
10350
10360.202
10370
1038-0.244
10390.405
1040
1040-0.333
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: CNhs11123

Jaspar motifP-value
MA0002.20.0362
MA0003.10.415
MA0004.10.7
MA0006.10.299
MA0007.10.662
MA0009.10.276
MA0014.10.341
MA0017.14.96926e-16
MA0018.21.18045e-5
MA0019.10.301
MA0024.10.71
MA0025.10.68
MA0027.10.999
MA0028.10.661
MA0029.10.0957
MA0030.10.285
MA0031.10.358
MA0035.21.29992e-6
MA0038.10.188
MA0039.20.584
MA0040.10.482
MA0041.10.312
MA0042.10.67
MA0043.10.0176
MA0046.13.96894e-56
MA0047.23.96348e-5
MA0048.10.208
MA0050.10.0595
MA0051.10.192
MA0052.10.00372
MA0055.10.368
MA0057.10.662
MA0058.10.603
MA0059.10.0897
MA0060.10.0815
MA0061.10.216
MA0062.20.891
MA0065.22.24468e-9
MA0066.10.0156
MA0067.10.0986
MA0068.10.708
MA0069.10.168
MA0070.10.78
MA0071.10.00169
MA0072.10.00184
MA0073.10.737
MA0074.10.297
MA0076.10.796
MA0077.10.0319
MA0078.10.754
MA0079.20.145
MA0080.20.208
MA0081.10.957
MA0083.10.132
MA0084.10.171
MA0087.10.0502
MA0088.10.31
MA0090.10.956
MA0091.10.455
MA0092.10.105
MA0093.10.736
MA0099.20.61
MA0100.10.897
MA0101.10.793
MA0102.20.317
MA0103.10.294
MA0104.20.759
MA0105.19.60218e-4
MA0106.10.0834
MA0107.10.93
MA0108.20.165
MA0111.10.966
MA0112.24.60811e-6
MA0113.10.39
MA0114.11.34213e-14
MA0115.14.77723e-10
MA0116.10.00791
MA0117.10.986
MA0119.10.00628
MA0122.10.329
MA0124.10.643
MA0125.10.893
MA0131.10.898
MA0135.10.157
MA0136.10.853
MA0137.20.48
MA0138.20.712
MA0139.10.0734
MA0140.17.39085e-13
MA0141.12.55471e-5
MA0142.10.32
MA0143.10.127
MA0144.10.569
MA0145.10.317
MA0146.10.251
MA0147.10.625
MA0148.12.097e-7
MA0149.10.0343
MA0150.10.0401
MA0152.10.864
MA0153.16.80349e-43
MA0154.10.0185
MA0155.10.526
MA0156.10.894
MA0157.10.313
MA0159.10.00283
MA0160.10.00359
MA0162.10.351
MA0163.12.40476e-5
MA0164.10.714
MA0258.10.00506
MA0259.10.864



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: CNhs11123

Novel motifP-value
10.0727
100.111
1000.54
1010.985
1020.216
1030.00503
1040.732
1050.935
1060.0549
1070.0418
1080.554
1090.0229
110.0722
1100.0588
1110.0232
1120.00535
1130.813
1140.0586
1150.924
1160.677
1170.0209
1180.177
1190.0919
120.716
1200.563
1210.766
1220.633
1230.234
1240.287
1250.828
1260.136
1270.581
1280.0381
1290.38
136.43339e-4
1300.667
1310.42
1320.867
1330.158
1340.392
1350.529
1360.605
1370.46
1380.393
1390.469
140.705
1400.0279
1410.787
1420.182
1430.459
1440.853
1450.0308
1460.352
1470.587
1480.661
1490.728
150.118
1500.176
1510.452
1520.216
1530.276
1540.657
1550.528
1560.113
1570.826
1580.867
1590.992
1600.138
1610.833
1620.643
1630.478
1640.0362
1650.339
1660.674
1670.108
1680.56
1690.00171
170.0716
180.458
190.0392
20.995
200.426
210.992
220.222
230.425
240.237
250.737
261.00678e-4
270.713
280.503
290.077
30.0221
300.992
310.38
320.154
330.259
340.899
350.588
360.0216
370.0742
380.383
390.305
40.599
400.161
410.776
420.16
430.0725
440.0793
450.855
460.0646
470.209
480.148
490.0605
50.13
500.571
510.344
520.372
530.867
540.338
550.542
560.344
570.447
580.372
590.214
60.885
600.155
610.228
620.119
630.124
640.444
650.247
660.889
670.496
680.183
690.577
70.131
700.167
710.0259
720.627
730.145
740.599
750.047
760.755
770.441
780.0213
790.934
80.00754
800.263
810.664
820.0972
830.867
840.866
850.107
860.261
870.76
880.845
890.191
90.594
900.0785
910.146
920.157
930.324
940.693
950.175
960.13
970.644
980.239
990.118



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: CNhs11123


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
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
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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