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|name=Follicle Associated Epithelium, pool3
|name=Follicle Associated Epithelium, pool3
|sample_id=10263
|sample_id=10263
|rna_tube_id=
|rna_tube_id=104D2
|rna_box=104
|rna_box=104
|rna_position=D2
|rna_position=D2
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=0.84000
|rna_od260/230=0.84
|rna_od260/280=2.22000
|rna_od260/280=2.22
|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=1.11760
|rna_weight_ug=1.1176
|rna_concentration=
|rna_concentration=0.1016
|sample_note=
|sample_note=
|profile_hcage=CNhs13200,LSID1004,,MAPPING
|profile_hcage=CNhs13200,LSID1004,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:37, 27 February 2012


Name:Follicle Associated Epithelium, pool3
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_c
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

CNhs13200

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.022
1006-0.346
1007-0.108
10081.953
1009-0.19
101-0.0984
10100
1011-0.337
10120
10130.309
1014-0.0874
1015-0.236
1016-0.563
10170
10180.486
10190
1020
10200
10210.332
1022-0.0343
10230
1024-0.185
1025-0.0611
10260
1027-0.048
10280
1029-0.0872
103-0.0887
10300
1031-0.911
10320.916
10330.0232
10340
10350
10360.0746
10370
1038-0.153
10390.0676
1040
1040-0.756
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: CNhs13200

Jaspar motifP-value
MA0002.20.00293
MA0003.10.246
MA0004.10.917
MA0006.10.106
MA0007.10.504
MA0009.10.591
MA0014.10.185
MA0017.14.5492e-18
MA0018.20.168
MA0019.10.113
MA0024.10.0666
MA0025.10.724
MA0027.10.886
MA0028.10.0516
MA0029.10.664
MA0030.10.495
MA0031.10.877
MA0035.20.00153
MA0038.10.379
MA0039.25.39073e-4
MA0040.10.142
MA0041.10.431
MA0042.10.666
MA0043.10.0651
MA0046.11.20768e-34
MA0047.20.068
MA0048.10.595
MA0050.11.11319e-4
MA0051.16.48562e-4
MA0052.11.98769e-4
MA0055.10.691
MA0057.10.0985
MA0058.10.985
MA0059.10.538
MA0060.10.00903
MA0061.10.00468
MA0062.27.63928e-5
MA0065.22.65542e-10
MA0066.10.121
MA0067.10.446
MA0068.10.365
MA0069.10.804
MA0070.10.0625
MA0071.10.212
MA0072.10.714
MA0073.10.892
MA0074.10.325
MA0076.10.126
MA0077.10.874
MA0078.10.49
MA0079.20.457
MA0080.27.03977e-10
MA0081.10.257
MA0083.10.0116
MA0084.10.592
MA0087.10.837
MA0088.10.184
MA0090.10.695
MA0091.10.521
MA0092.10.417
MA0093.10.976
MA0099.21.60766e-6
MA0100.10.747
MA0101.10.00153
MA0102.20.37
MA0103.12.11984e-6
MA0104.20.502
MA0105.10.00551
MA0106.10.152
MA0107.10.00274
MA0108.20.815
MA0111.10.916
MA0112.24.2466e-4
MA0113.10.447
MA0114.11.02686e-18
MA0115.11.99914e-11
MA0116.10.0782
MA0117.10.91
MA0119.10.185
MA0122.10.704
MA0124.10.22
MA0125.10.215
MA0131.10.906
MA0135.10.353
MA0136.16.63414e-16
MA0137.20.0811
MA0138.20.725
MA0139.10.0493
MA0140.10.122
MA0141.11.12699e-4
MA0142.10.123
MA0143.10.137
MA0144.10.0269
MA0145.10.0281
MA0146.10.228
MA0147.10.752
MA0148.10.0257
MA0149.10.00814
MA0150.10.0301
MA0152.10.0866
MA0153.19.23756e-31
MA0154.10.0126
MA0155.10.758
MA0156.14.57649e-8
MA0157.10.687
MA0159.12.39489e-4
MA0160.10.00531
MA0162.10.276
MA0163.10.012
MA0164.10.505
MA0258.10.0256
MA0259.10.624



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: CNhs13200

Novel motifP-value
10.109
100.123
1000.79
1010.918
1020.959
1030.118
1040.765
1050.449
1060.0427
1070.178
1080.838
1090.0223
110.102
1100.25
1110.0548
1120.014
1130.542
1140.0738
1150.546
1160.202
1170.0297
1180.297
1190.0778
120.649
1200.555
1210.385
1220.987
1230.104
1240.542
1250.681
1260.0829
1270.253
1280.094
1290.0919
130.00125
1300.865
1310.955
1320.593
1330.861
1340.999
1350.105
1360.0725
1370.963
1380.438
1390.104
140.663
1400.198
1410.139
1420.597
1430.764
1440.245
1450.124
1460.393
1470.743
1480.451
1490.932
150.141
1500.448
1510.544
1520.0639
1530.594
1540.899
1550.289
1560.0393
1570.47
1580.645
1590.542
1600.629
1610.388
1620.476
1630.267
1640.154
1650.0651
1660.611
1670.545
1680.974
1690.0129
170.0497
180.705
190.237
20.817
200.616
210.45
220.345
230.639
240.743
250.435
260.00597
270.606
280.363
290.0576
30.0646
300.467
310.69
320.0934
330.209
340.909
350.482
360.201
370.0386
380.385
390.381
40.407
400.172
410.451
420.392
430.181
440.0501
450.49
460.178
470.216
480.141
490.233
50.421
500.44
510.656
520.233
530.52
540.557
550.968
560.384
570.89
580.259
590.136
60.511
600.0495
610.185
620.14
630.121
640.638
650.228
660.934
670.506
680.0133
690.849
70.085
700.00417
710.0654
720.406
730.0381
740.508
750.0132
760.534
770.13
780.0301
790.659
80.0787
800.631
810.695
820.0898
830.0514
840.434
850.0694
860.15
870.014
880.536
890.185
90.878
900.0303
910.462
920.372
930.283
940.471
950.0241
960.72
970.899
980.359
990.305



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: CNhs13200


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)
0000119 (cell layer)
0000344 (mucosa)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
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))
0003199 (egg chamber)
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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