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|name=GP2+ M cell, pool1
|name=GP2+ M cell, pool1
|sample_id=11845
|sample_id=11845
|rna_tube_id=
|rna_tube_id=124H9
|rna_box=124
|rna_box=124
|rna_position=H9
|rna_position=H9
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.36000
|rna_od260/230=1.36
|rna_od260/280=2.55000
|rna_od260/280=2.55
|sample_cell_type=M cell
|sample_cell_type=M cell
|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=0.24200
|rna_weight_ug=0.242
|rna_concentration=0.02200
|rna_concentration=0.022
|sample_note=
|sample_note=
|profile_hcage=CNhs13228,LSID1006,release012,MAPPING
|profile_hcage=CNhs13228,LSID1006,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:37, 27 February 2012


Name:GP2+ M cell, pool1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageadult
sexmale
ageNA
cell typeM cell
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberM cell_a
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

CNhs13228

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.179
1006-0.264
1007-0.0374
10081.218
1009-0.177
101-0.344
10100
1011-0.337
10120
10130.348
1014-0.0874
1015-0.428
1016-0.594
10170
10180.518
10190
1020
10200
10210
1022-0.0704
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.911
10321.065
10330
10340
10350
1036-0.0428
10370
1038-0.0166
10390.00176
1040
1040-0.728
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: CNhs13228

Jaspar motifP-value
MA0002.20.0107
MA0003.10.387
MA0004.10.845
MA0006.10.0771
MA0007.10.284
MA0009.10.0663
MA0014.10.0541
MA0017.14.20677e-29
MA0018.20.207
MA0019.10.0535
MA0024.14.97107e-4
MA0025.10.933
MA0027.10.895
MA0028.10.0769
MA0029.10.901
MA0030.10.635
MA0031.10.195
MA0035.26.97773e-6
MA0038.10.517
MA0039.25.01859e-6
MA0040.10.0777
MA0041.10.278
MA0042.10.286
MA0043.10.665
MA0046.11.37008e-49
MA0047.20.0231
MA0048.10.358
MA0050.10.00136
MA0051.14.56306e-5
MA0052.10.594
MA0055.10.256
MA0057.10.0752
MA0058.10.948
MA0059.10.736
MA0060.10.222
MA0061.10.00521
MA0062.23.44942e-4
MA0065.21.94103e-16
MA0066.10.126
MA0067.10.714
MA0068.10.0766
MA0069.10.741
MA0070.10.289
MA0071.10.042
MA0072.10.683
MA0073.10.829
MA0074.10.167
MA0076.10.204
MA0077.10.448
MA0078.10.892
MA0079.20.482
MA0080.24.3483e-5
MA0081.10.805
MA0083.10.396
MA0084.10.138
MA0087.10.295
MA0088.10.451
MA0090.10.462
MA0091.10.253
MA0092.10.404
MA0093.10.908
MA0099.21.30744e-11
MA0100.10.886
MA0101.16.14946e-5
MA0102.20.642
MA0103.11.47984e-6
MA0104.20.118
MA0105.10.157
MA0106.10.287
MA0107.17.56356e-5
MA0108.26.25441e-4
MA0111.10.424
MA0112.20.00268
MA0113.10.936
MA0114.12.75589e-34
MA0115.11.55177e-16
MA0116.10.388
MA0117.10.243
MA0119.10.0821
MA0122.10.816
MA0124.10.468
MA0125.10.92
MA0131.10.556
MA0135.10.392
MA0136.16.21259e-8
MA0137.20.017
MA0138.20.868
MA0139.10.201
MA0140.10.147
MA0141.18.01488e-8
MA0142.10.071
MA0143.10.233
MA0144.10.00173
MA0145.10.00795
MA0146.10.14
MA0147.10.156
MA0148.10.0239
MA0149.10.0187
MA0150.10.00498
MA0152.10.133
MA0153.19.61844e-42
MA0154.10.0444
MA0155.10.812
MA0156.13.03693e-4
MA0157.10.836
MA0159.11.56802e-4
MA0160.16.87295e-6
MA0162.10.68
MA0163.10.589
MA0164.10.995
MA0258.10.0614
MA0259.10.557



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: CNhs13228

Novel motifP-value
10.178
100.304
1000.867
1010.958
1020.799
1030.52
1040.88
1050.0859
1060.0128
1070.126
1080.597
1090.0469
110.13
1100.393
1110.216
1120.0177
1130.22
1140.12
1150.488
1160.095
1170.0564
1180.541
1190.141
120.74
1200.64
1210.378
1220.72
1230.134
1240.242
1250.716
1260.0476
1270.167
1280.176
1290.15
137.56184e-5
1300.938
1310.795
1320.6
1330.473
1340.752
1350.152
1360.0387
1370.977
1380.347
1390.093
140.63
1400.842
1410.108
1420.754
1430.237
1440.236
1450.112
1460.234
1470.588
1481
1490.844
150.129
1500.347
1510.799
1520.0231
1530.683
1540.644
1550.256
1560.19
1570.439
1580.444
1590.71
1600.799
1610.595
1620.99
1630.0778
1640.096
1650.129
1660.595
1670.997
1680.942
1690.0341
170.0304
180.979
190.325
20.706
200.361
210.968
220.256
230.268
240.611
250.463
260.021
270.921
280.269
290.155
30.154
300.282
310.854
320.198
330.208
340.857
350.849
360.647
370.0325
380.409
390.418
40.432
400.221
410.126
420.712
430.316
440.123
450.375
460.478
470.471
480.25
490.318
50.666
500.455
510.562
520.112
530.499
540.319
550.529
560.534
570.892
580.217
590.163
60.674
600.0294
610.436
620.204
630.123
640.702
650.279
660.813
670.583
680.125
690.931
70.0844
700.00307
710.21
720.293
730.0222
740.931
750.0261
760.939
770.0597
780.0296
790.868
80.389
800.886
810.906
820.0595
830.423
840.0673
850.117
860.11
870.0177
880.278
890.309
90.994
900.511
910.652
920.459
930.242
940.816
950.0043
960.64
970.914
980.447
990.35



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: CNhs13228


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000473 (defensive cell)
0000548 (animal cell)
0000627 (transporting cell)
0000682 (M cell of gut)
0002371 (somatic cell)

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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