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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11846
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11846
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11846
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11846
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool2.CNhs13231.11846-124I1.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool2.CNhs13231.11846-124I1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool2.CNhs13231.11846-124I1.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool2.CNhs13231.11846-124I1.mm10.nobarcode.ctss.bed.gz

Revision as of 17:13, 4 August 2017


Name:GP2+ M cell, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13231
Sample type:primary cells
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_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005557
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13231 CAGE DRX008766 DRR009638
Accession ID Mm9

Library idBAMCTSS
CNhs13231 DRZ001063 DRZ002448
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs13231

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.123
10040
10051.267
1006-0.436
1007-0.0093
10081.685
1009-0.19
101-0.243
10100
1011-0.337
10120
10130.31
1014-0.0874
1015-0.325
1016-0.581
10170
10180.604
10190
1020
10200
10210
1022-0.0704
10230
1024-0.2
10250
10260
1027-0.048
10280
1029-0.148
103-0.0887
10300
1031-0.961
10321.045
10330
10340
10350
1036-0.183
10370
10380.0712
10390.08
1040
1040-0.983
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



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: CNhs13231

Jaspar motifP-value
MA0002.20.0186
MA0003.10.342
MA0004.10.691
MA0006.10.0783
MA0007.10.178
MA0009.10.166
MA0014.10.0838
MA0017.11.80682e-28
MA0018.20.596
MA0019.10.0509
MA0024.10.00476
MA0025.10.533
MA0027.10.933
MA0028.10.0437
MA0029.10.963
MA0030.10.478
MA0031.10.349
MA0035.26.03306e-5
MA0038.10.452
MA0039.29.58271e-6
MA0040.10.0959
MA0041.10.223
MA0042.10.222
MA0043.10.749
MA0046.11.08992e-55
MA0047.20.0085
MA0048.10.28
MA0050.12.21285e-4
MA0051.11.09003e-5
MA0052.10.389
MA0055.10.253
MA0057.10.0717
MA0058.10.801
MA0059.10.831
MA0060.10.0892
MA0061.10.00232
MA0062.27.52286e-5
MA0065.22.17264e-15
MA0066.10.0648
MA0067.10.999
MA0068.10.101
MA0069.10.617
MA0070.10.135
MA0071.10.0303
MA0072.10.94
MA0073.10.844
MA0074.10.244
MA0076.10.135
MA0077.10.442
MA0078.10.507
MA0079.20.468
MA0080.22.12839e-5
MA0081.10.954
MA0083.10.46
MA0084.10.208
MA0087.10.238
MA0088.10.243
MA0090.10.471
MA0091.10.323
MA0092.10.595
MA0093.10.759
MA0099.27.2398e-11
MA0100.10.723
MA0101.16.52458e-6
MA0102.20.564
MA0103.17.95617e-7
MA0104.20.263
MA0105.10.115
MA0106.10.296
MA0107.18.79905e-6
MA0108.20.0014
MA0111.10.593
MA0112.20.00189
MA0113.10.55
MA0114.17.3462e-33
MA0115.17.95636e-15
MA0116.10.303
MA0117.10.385
MA0119.10.0743
MA0122.10.786
MA0124.10.596
MA0125.10.678
MA0131.10.721
MA0135.10.243
MA0136.11.21742e-9
MA0137.20.0082
MA0138.20.896
MA0139.10.193
MA0140.10.151
MA0141.11.63856e-7
MA0142.10.0786
MA0143.10.229
MA0144.10.00134
MA0145.10.014
MA0146.10.0744
MA0147.10.341
MA0148.10.00633
MA0149.10.0403
MA0150.10.013
MA0152.10.105
MA0153.17.69532e-45
MA0154.10.075
MA0155.10.832
MA0156.16.74088e-5
MA0157.10.817
MA0159.11.85653e-4
MA0160.12.33813e-5
MA0162.10.762
MA0163.10.416
MA0164.10.917
MA0258.10.0289
MA0259.10.663



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: CNhs13231

Novel motifP-value
10.168
100.284
1000.881
1010.783
1020.888
1030.382
1040.998
1050.112
1060.0107
1070.123
1080.645
1090.031
110.142
1100.466
1110.121
1120.0164
1130.206
1140.145
1150.857
1160.0785
1170.0343
1180.579
1190.144
120.583
1200.692
1210.338
1220.951
1230.0733
1240.227
1250.234
1260.0582
1270.187
1280.134
1290.127
139.40537e-5
1300.807
1310.746
1320.639
1330.293
1340.917
1350.135
1360.0155
1370.765
1380.155
1390.143
140.67
1400.804
1410.125
1420.841
1430.219
1440.287
1450.167
1460.21
1470.59
1480.695
1490.804
150.123
1500.405
1510.847
1520.0159
1530.77
1540.758
1550.289
1560.0964
1570.34
1580.561
1590.627
1600.705
1610.788
1620.772
1630.251
1640.1
1650.09
1660.916
1670.787
1680.91
1690.0331
170.0274
180.999
190.314
20.685
200.322
210.998
220.241
230.455
240.548
250.446
260.0115
270.957
280.324
290.0686
30.207
300.372
310.774
320.363
330.275
340.729
350.833
360.584
370.0324
380.421
390.441
40.261
400.176
410.0953
420.716
430.288
440.277
450.337
460.368
470.48
480.264
490.351
50.633
500.417
510.605
520.128
530.509
540.391
550.541
560.502
570.94
580.239
590.243
60.638
600.0314
610.341
620.214
630.0955
640.752
650.284
660.997
670.655
680.0548
690.988
70.0672
700.00331
710.153
720.3
730.0183
740.981
750.0184
760.689
770.0711
780.0267
790.924
80.279
800.749
810.955
820.0942
830.334
840.0759
850.115
860.139
870.0115
880.268
890.247
90.94
900.335
910.66
920.54
930.222
940.783
950.00465
960.922
970.809
980.626
990.418



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: CNhs13231


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

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

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0011159 (mouse GP2-positive M cell 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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