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|name=Follicle Associated Epithelium, pool2
|name=Follicle Associated Epithelium, pool2
|sample_id=10262
|sample_id=10262
|rna_tube_id=
|rna_tube_id=104D1
|rna_box=104
|rna_box=104
|rna_position=D1
|rna_position=D1
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.61000
|rna_od260/230=1.61
|rna_od260/280=2.14000
|rna_od260/280=2.14
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_cell_line=
Line 29: Line 29:
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=2.20550
|rna_weight_ug=2.2055
|rna_concentration=
|rna_concentration=0.2005
|sample_note=
|sample_note=
|profile_hcage=CNhs13211,LSID1005,,MAPPING
|profile_hcage=CNhs13211,LSID1005,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:37, 27 February 2012


Name:Follicle Associated Epithelium, pool2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissuePeyer's patch
dev stageNA
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberFAE_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13211

00
10
100
1000
1000-0.00325
1001-0.0346
1002-0.116
1003-0.125
10040
10051.03
1006-0.326
1007-0.141
10082.03
1009-0.19
101-0.0559
10100
1011-0.217
10120
10130.294
1014-0.0874
1015-0.184
1016-0.484
10170
10180.589
10190
1020
10200
10210.244
1022-0.0956
10230
1024-0.305
10250
10260
1027-0.048
10280
1029-0.0623
103-0.0887
10300.0645
1031-0.911
10320.758
1033-0.00204
10340.0344
10350
1036-0.167
10370
1038-0.178
10390.0463
1040.0645
1040-0.678
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: CNhs13211

Jaspar motifP-value
MA0002.20.00228
MA0003.10.222
MA0004.10.988
MA0006.10.116
MA0007.10.619
MA0009.10.549
MA0014.10.262
MA0017.18.17881e-19
MA0018.20.121
MA0019.10.109
MA0024.10.0843
MA0025.10.823
MA0027.10.942
MA0028.10.0635
MA0029.10.909
MA0030.10.514
MA0031.10.817
MA0035.26.83603e-4
MA0038.10.287
MA0039.20.00104
MA0040.10.253
MA0041.10.33
MA0042.10.514
MA0043.10.0333
MA0046.14.82555e-36
MA0047.20.0626
MA0048.10.599
MA0050.13.08958e-4
MA0051.10.00108
MA0052.12.54624e-4
MA0055.10.722
MA0057.10.12
MA0058.10.925
MA0059.10.491
MA0060.10.00455
MA0061.10.00443
MA0062.21.06509e-4
MA0065.29.03496e-11
MA0066.10.0779
MA0067.10.389
MA0068.10.147
MA0069.10.836
MA0070.10.0641
MA0071.10.21
MA0072.10.82
MA0073.10.764
MA0074.10.355
MA0076.10.134
MA0077.10.894
MA0078.10.547
MA0079.20.424
MA0080.25.36858e-10
MA0081.10.251
MA0083.10.00391
MA0084.10.551
MA0087.10.678
MA0088.10.177
MA0090.10.67
MA0091.10.536
MA0092.10.419
MA0093.10.956
MA0099.21.54722e-6
MA0100.10.673
MA0101.10.00206
MA0102.20.339
MA0103.12.00811e-6
MA0104.20.49
MA0105.10.00331
MA0106.10.199
MA0107.10.00295
MA0108.20.778
MA0111.10.915
MA0112.23.38454e-4
MA0113.10.481
MA0114.11.22626e-19
MA0115.12.93576e-12
MA0116.10.0503
MA0117.10.869
MA0119.10.182
MA0122.10.533
MA0124.10.251
MA0125.10.281
MA0131.10.794
MA0135.10.413
MA0136.11.10831e-16
MA0137.20.0982
MA0138.20.78
MA0139.10.0483
MA0140.10.104
MA0141.11.08004e-4
MA0142.10.111
MA0143.10.114
MA0144.10.0298
MA0145.10.0288
MA0146.10.216
MA0147.10.73
MA0148.10.0226
MA0149.10.0216
MA0150.10.0273
MA0152.10.113
MA0153.11.13201e-33
MA0154.10.0103
MA0155.10.743
MA0156.17.232e-9
MA0157.10.725
MA0159.12.21594e-4
MA0160.10.00442
MA0162.10.287
MA0163.10.00605
MA0164.10.464
MA0258.10.0172
MA0259.10.584



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: CNhs13211

Novel motifP-value
10.116
100.0981
1000.85
1010.797
1020.894
1030.0831
1040.833
1050.538
1060.0401
1070.179
1080.744
1090.0258
110.0966
1100.188
1110.0422
1120.013
1130.647
1140.0503
1150.541
1160.191
1170.0302
1180.312
1190.0666
120.576
1200.387
1210.377
1220.915
1230.115
1240.626
1250.53
1260.118
1270.173
1280.12
1290.104
130.00126
1300.877
1310.921
1320.788
1330.89
1340.905
1350.139
1360.0981
1370.796
1380.292
1390.118
140.739
1400.113
1410.0922
1420.396
1430.806
1440.232
1450.0756
1460.427
1470.991
1480.379
1490.907
150.145
1500.434
1510.504
1520.0729
1530.703
1540.915
1550.395
1560.0445
1570.504
1580.732
1590.705
1600.561
1610.397
1620.456
1630.31
1640.151
1650.134
1660.577
1670.511
1680.907
1690.0116
170.0621
180.711
190.233
20.735
200.683
210.495
220.348
230.625
240.712
250.425
260.00814
270.576
280.39
290.0557
30.0824
300.439
310.806
320.107
330.216
340.88
350.416
360.231
370.0387
380.401
390.395
40.344
400.173
410.463
420.442
430.188
440.0229
450.479
460.171
470.193
480.13
490.242
50.442
500.458
510.641
520.244
530.525
540.507
550.891
560.391
570.95
580.252
590.116
60.467
600.0478
610.259
620.124
630.121
640.612
650.231
660.975
670.47
680.019
690.716
70.0692
700.00519
710.0658
720.4
730.0517
740.422
750.018
760.638
770.109
780.0275
790.601
80.0988
800.679
810.743
820.045
830.113
840.217
850.0916
860.139
870.0232
880.428
890.193
90.832
900.0467
910.563
920.286
930.224
940.574
950.0283
960.735
970.864
980.322
990.267



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: CNhs13211


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)
0000064 (organ part)
0000344 (mucosa)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0001744 (lymphoid tissue)
0001961 (mucosa-associated lymphoid tissue)
0001962 (gut-associated lymphoid tissue)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002405 (immune system)
0002465 (lymphoid system)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)

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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