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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008659
|DRA_sample_Accession=CAGE@SAMD00005052
|accession_numbers=CAGE;DRX008769;DRR009641;DRZ001066;DRZ002451
|accession_numbers=CAGE;DRX008769;DRR009641;DRZ001066;DRZ002451
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409

Revision as of 21:16, 31 July 2014


Name:Lgr5 positive intestinal stem cells, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs12555
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesmall intestine
dev stageNA
sexmale
ageNA
cell typestem cell
cell lineNA
companyNA
collaborationMarc van de Wetering
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005052
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12555 CAGE DRX008769 DRR009641
Accession ID Mm9

Library idBAMCTSS
CNhs12555 DRZ001066 DRZ002451
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

CNhs12555

00
10
100
1000
1000-0.0355
1001-0.0668
1002-0.116
1003-0.109
10040
10050.11
1006-0.143
1007-0.0809
10080.883
1009-0.19
1010.13
10100
1011-0.298
10120
1013-0.136
1014-0.0874
1015-0.143
1016-0.426
10170
10180.437
10190
1020
10200
10210
10220.218
10230
1024-0.172
10250
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-1.033
10320.431
10330.575
10340
10350
10360.452
10370
1038-0.12
10390.103
1040
1040-0.811
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: CNhs12555

Jaspar motifP-value
MA0002.20.368
MA0003.10.798
MA0004.10.0111
MA0006.10.962
MA0007.10.141
MA0009.10.172
MA0014.10.0615
MA0017.12.12026e-13
MA0018.21.46134e-5
MA0019.10.625
MA0024.14.53992e-5
MA0025.10.025
MA0027.10.224
MA0028.11.80788e-9
MA0029.10.12
MA0030.10.389
MA0031.10.109
MA0035.26.67734e-4
MA0038.10.174
MA0039.21.31569e-4
MA0040.10.123
MA0041.10.135
MA0042.10.436
MA0043.16.61037e-6
MA0046.15.84292e-42
MA0047.25.83788e-4
MA0048.10.0138
MA0050.10.0122
MA0051.10.00668
MA0052.10.0921
MA0055.14.4324e-5
MA0057.10.198
MA0058.10.00862
MA0059.10.00188
MA0060.16.38026e-9
MA0061.10.156
MA0062.21.83612e-12
MA0065.21.60445e-6
MA0066.10.81
MA0067.10.218
MA0068.10.923
MA0069.10.425
MA0070.10.503
MA0071.10.0274
MA0072.10.672
MA0073.10.878
MA0074.10.797
MA0076.15.82987e-9
MA0077.10.279
MA0078.10.361
MA0079.20.289
MA0080.20.00234
MA0081.10.862
MA0083.10.154
MA0084.10.0585
MA0087.10.167
MA0088.10.0193
MA0090.10.595
MA0091.10.24
MA0092.10.179
MA0093.10.0124
MA0099.20.0741
MA0100.10.073
MA0101.10.00875
MA0102.20.675
MA0103.15.32734e-6
MA0104.20.0211
MA0105.10.128
MA0106.10.43
MA0107.10.044
MA0108.20.361
MA0111.10.464
MA0112.20.176
MA0113.10.312
MA0114.12.09187e-15
MA0115.15.01733e-9
MA0116.10.082
MA0117.10.884
MA0119.10.607
MA0122.10.238
MA0124.10.692
MA0125.10.59
MA0131.10.0951
MA0135.10.436
MA0136.13.12593e-11
MA0137.29.20984e-5
MA0138.20.0748
MA0139.10.129
MA0140.10.484
MA0141.16.27359e-4
MA0142.10.108
MA0143.10.3
MA0144.10.00805
MA0145.10.809
MA0146.10.154
MA0147.10.00744
MA0148.18.08488e-4
MA0149.10.00797
MA0150.10.564
MA0152.10.456
MA0153.15.83854e-30
MA0154.10.88
MA0155.10.477
MA0156.11.20242e-7
MA0157.10.551
MA0159.10.00201
MA0160.15.42802e-4
MA0162.10.955
MA0163.10.0156
MA0164.10.805
MA0258.10.382
MA0259.10.136



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: CNhs12555

Novel motifP-value
10.42
100.0665
1000.273
1010.327
1020.885
1030.515
1040.938
1050.486
1060.438
1070.946
1080.509
1090.0503
110.337
1100.122
1110.35
1120.142
1130.0526
1140.52
1150.395
1160.829
1170.0077
1180.485
1190.937
120.834
1200.769
1210.308
1220.847
1230.0304
1240.0304
1250.105
1260.00355
1270.753
1280.835
1290.916
133.09425e-7
1300.241
1310.828
1320.33
1330.462
1340.262
1350.0712
1360.00466
1370.424
1380.461
1390.319
140.724
1400.985
1410.366
1420.911
1430.0346
1440.0176
1450.0218
1460.437
1470.8
1480.52
1490.231
150.338
1500.508
1510.767
1520.5
1530.918
1540.814
1550.871
1560.215
1570.407
1580.309
1590.833
1600.981
1610.711
1620.224
1630.695
1640.147
1650.238
1660.721
1670.263
1680.805
1690.158
170.204
180.151
190.77
20.25
200.0776
210.771
220.999
230.27
240.0885
250.127
260.00684
270.787
280.95
290.00903
30.351
300.875
310.326
320.237
330.053
340.367
350.827
360.107
370.235
380.678
390.628
40.61
400.0615
410.239
420.767
430.802
440.979
450.851
460.437
470.598
480.276
490.897
50.849
500.985
510.856
520.782
530.495
540.978
550.705
560.936
570.742
580.285
590.732
60.572
600.198
610.305
620.261
630.5
640.645
650.909
660.337
670.694
680.661
690.176
70.0168
700.234
710.0382
720.408
730.0721
740.525
750.0132
760.618
770.665
780.0285
790.746
80.333
800.589
810.483
820.791
830.498
840.755
850.743
860.369
870.00428
880.52
890.975
90.693
900.104
910.0323
920.121
930.142
940.401
950.00292
960.597
970.994
980.557
990.753



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: CNhs12555


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002250 (intestinal crypt stem cell)

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)
0000079 (mouse Lgr5-positive intestinal epithelial stem 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
CL:0000223 (endodermal cell)

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