Personal tools

FF:11850-124I5

From FANTOM5_SSTAR

Revision as of 09:53, 28 November 2014 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs13242
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageadult
sexmale
ageNA
cell typeenterocyte
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRANKL_Ep+_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005872
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13242 CAGE DRX008762 DRR009634
Accession ID Mm9

Library idBAMCTSS
CNhs13242 DRZ001059 DRZ002444
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs13242

00
10
100
1000
1000-0.0355
1001-0.0706
1002-0.116
1003-0.156
10040
10050.943
1006-0.42
10070.217
10081.06
1009-0.19
101-0.409
10100
1011-0.337
10120
10130.419
1014-0.0874
1015-0.364
1016-0.465
10170
10180.579
10190
1020
10200
10210
10220
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.176
103-0.0848
10300
1031-0.781
10321.094
10330
10340
10350
1036-0.183
10370
10380.157
10390.0126
1040
1040-0.376
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: CNhs13242

Jaspar motifP-value
MA0002.20.0181
MA0003.10.377
MA0004.10.718
MA0006.10.0454
MA0007.10.277
MA0009.10.152
MA0014.10.05
MA0017.15.43916e-34
MA0018.20.0267
MA0019.10.0258
MA0024.12.55729e-5
MA0025.10.248
MA0027.10.676
MA0028.10.0377
MA0029.10.892
MA0030.10.345
MA0031.10.201
MA0035.23.27086e-6
MA0038.10.686
MA0039.27.2344e-6
MA0040.10.178
MA0041.10.22
MA0042.10.271
MA0043.10.11
MA0046.14.40257e-51
MA0047.20.0328
MA0048.10.276
MA0050.11.69843e-4
MA0051.11.06129e-6
MA0052.10.957
MA0055.10.239
MA0057.10.053
MA0058.10.817
MA0059.10.391
MA0060.10.841
MA0061.10.00179
MA0062.24.08608e-5
MA0065.26.59578e-17
MA0066.10.124
MA0067.10.375
MA0068.10.11
MA0069.10.899
MA0070.10.384
MA0071.10.0472
MA0072.10.827
MA0073.10.912
MA0074.10.369
MA0076.10.0857
MA0077.10.46
MA0078.10.806
MA0079.20.0769
MA0080.29.02861e-5
MA0081.10.89
MA0083.10.697
MA0084.10.192
MA0087.10.278
MA0088.10.748
MA0090.10.319
MA0091.10.0398
MA0092.10.708
MA0093.10.756
MA0099.21.49328e-14
MA0100.10.793
MA0101.12.48815e-6
MA0102.20.836
MA0103.12.31916e-6
MA0104.20.0729
MA0105.10.479
MA0106.10.615
MA0107.11.04385e-6
MA0108.23.0289e-4
MA0111.10.357
MA0112.20.0174
MA0113.10.939
MA0114.13.31427e-42
MA0115.16.66596e-18
MA0116.10.905
MA0117.10.137
MA0119.10.0959
MA0122.10.935
MA0124.10.667
MA0125.10.852
MA0131.10.628
MA0135.10.177
MA0136.14.58941e-8
MA0137.20.0226
MA0138.20.975
MA0139.10.338
MA0140.10.0849
MA0141.11.85482e-7
MA0142.10.0154
MA0143.10.11
MA0144.10.00171
MA0145.10.00394
MA0146.10.0882
MA0147.10.0679
MA0148.10.048
MA0149.10.0411
MA0150.10.00367
MA0152.10.178
MA0153.11.35869e-42
MA0154.10.103
MA0155.10.776
MA0156.11.43499e-5
MA0157.10.908
MA0159.18.89128e-4
MA0160.11.73404e-6
MA0162.10.91
MA0163.10.735
MA0164.10.799
MA0258.10.133
MA0259.10.467



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: CNhs13242

Novel motifP-value
10.306
100.556
1000.818
1010.852
1020.848
1030.945
1040.646
1050.114
1060.0171
1070.162
1080.411
1090.109
110.261
1100.584
1110.202
1120.045
1130.255
1140.278
1150.501
1160.0746
1170.089
1180.713
1190.158
120.656
1200.526
1210.265
1220.601
1230.0899
1240.279
1250.648
1260.102
1270.164
1280.138
1290.291
131.87764e-5
1300.639
1310.949
1320.586
1330.416
1340.793
1350.112
1360.00993
1370.765
1380.231
1390.251
140.69
1400.73
1410.292
1420.655
1430.119
1440.252
1450.236
1460.231
1470.744
1480.995
1490.902
150.221
1500.327
1510.947
1520.0201
1530.582
1540.556
1550.37
1560.163
1570.325
1580.465
1590.697
1600.394
1610.801
1620.745
1630.057
1640.247
1650.261
1660.709
1670.786
1680.965
1690.0904
170.0322
180.801
190.413
20.58
200.317
210.93
220.211
230.223
240.805
250.472
260.0257
270.634
280.22
290.314
30.306
300.217
310.899
320.484
330.225
340.92
350.876
360.647
370.0237
380.534
390.448
40.394
400.391
410.219
420.861
430.438
440.264
450.223
460.65
470.691
480.39
490.534
50.977
500.355
510.697
520.106
530.483
540.342
550.438
560.668
570.506
580.314
590.218
60.724
600.0214
610.64
620.282
630.147
640.914
650.396
660.682
670.398
680.0496
690.94
70.0651
700.0165
710.423
720.359
730.0132
740.708
750.0413
760.987
770.0494
780.0219
790.682
80.936
800.958
810.945
820.0711
830.703
840.0341
850.126
860.0945
870.0057
880.207
890.627
90.986
900.938
910.902
920.704
930.262
940.407
950.0054
960.897
970.855
980.594
990.634



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: CNhs13242


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)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
0000677 (gut absorptive cell)
0000212 (absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0000584 (enterocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000160 (intestine)
0000483 (epithelium)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000383 (3 days sample)
0000627 (RANK ligand treatment sample)
0011113 (mouse CD326-positive enterocyte isolated from mice- treated with RANKL- day03 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
CL:0000223 (endodermal cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11850-124I5&oldid=3283253"