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FF:860-29I3: Difference between revisions

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|library_id=CNhs10506
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|library_id_phase_based=1:CNhs10506
|name=intestinal mucosa, adult
|name=intestinal mucosa, adult
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:04, 18 June 2014


Name:intestinal mucosa, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10506
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestinal mucosa
dev stageadult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008851
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10506 CAGE DRX008988 DRR009862
Accession ID Mm9

Library idBAMCTSS
CNhs10506 DRZ001287 DRZ002670
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

CNhs10506

00
10
100
1000
1000-0.0355
10010.0102
1002-0.116
1003-0.102
10040
10050.35
1006-0.143
1007-0.104
10080.798
1009-0.19
101-0.375
10100
1011-0.145
10120
10130.41
10140
1015-0.54
1016-0.379
10170
10180.666
10190
1020
10200
1021-0.0487
10220.0211
10230
1024-0.307
10250
10260
1027-0.048
10280
10290.483
103-0.0861
10300
1031-0.972
10320.635
1033-0.0396
10340.203
10350
1036-0.436
10370
10380.0449
1039-0.0905
1040
1040-0.676
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: CNhs10506

Jaspar motifP-value
MA0002.24.45167e-4
MA0003.10.346
MA0004.10.636
MA0006.10.0606
MA0007.10.384
MA0009.10.26
MA0014.10.289
MA0017.15.6012e-27
MA0018.20.166
MA0019.10.298
MA0024.15.15593e-4
MA0025.10.799
MA0027.10.263
MA0028.10.844
MA0029.10.641
MA0030.10.618
MA0031.10.4
MA0035.23.78852e-6
MA0038.10.138
MA0039.24.247e-4
MA0040.10.0444
MA0041.10.366
MA0042.10.259
MA0043.10.0615
MA0046.18.27811e-44
MA0047.20.00474
MA0048.10.583
MA0050.18.84252e-8
MA0051.16.99028e-7
MA0052.18.74771e-4
MA0055.10.362
MA0057.10.0702
MA0058.10.547
MA0059.10.753
MA0060.13.38685e-5
MA0061.10.353
MA0062.20.126
MA0065.28.00267e-15
MA0066.10.0665
MA0067.10.537
MA0068.10.00666
MA0069.10.46
MA0070.10.223
MA0071.10.127
MA0072.10.297
MA0073.10.905
MA0074.10.135
MA0076.10.986
MA0077.10.767
MA0078.10.674
MA0079.20.636
MA0080.22.28524e-6
MA0081.10.654
MA0083.10.034
MA0084.10.265
MA0087.10.454
MA0088.10.469
MA0090.10.642
MA0091.10.941
MA0092.10.428
MA0093.10.62
MA0099.28.98089e-5
MA0100.10.323
MA0101.10.715
MA0102.20.131
MA0103.13.92535e-6
MA0104.20.0696
MA0105.10.314
MA0106.10.839
MA0107.10.836
MA0108.20.52
MA0111.10.847
MA0112.21.04135e-5
MA0113.10.484
MA0114.11.94385e-29
MA0115.11.59586e-16
MA0116.10.409
MA0117.10.454
MA0119.10.0174
MA0122.10.76
MA0124.10.263
MA0125.10.742
MA0131.10.416
MA0135.10.228
MA0136.18.45297e-7
MA0137.20.381
MA0138.20.376
MA0139.10.0305
MA0140.10.00968
MA0141.16.44861e-7
MA0142.10.905
MA0143.10.15
MA0144.10.0597
MA0145.10.00322
MA0146.10.109
MA0147.10.0972
MA0148.11.88116e-4
MA0149.10.0112
MA0150.10.0367
MA0152.10.0543
MA0153.14.75446e-36
MA0154.10.0258
MA0155.10.686
MA0156.13.55098e-4
MA0157.10.95
MA0159.13.09495e-4
MA0160.19.73291e-4
MA0162.10.604
MA0163.10.121
MA0164.10.907
MA0258.19.12915e-4
MA0259.10.273



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: CNhs10506

Novel motifP-value
10.0831
100.133
1000.872
1010.845
1020.893
1030.116
1040.899
1050.258
1060.0445
1070.0857
1080.802
1090.124
110.116
1100.253
1110.0159
1120.0144
1130.88
1140.0113
1150.813
1160.446
1170.0883
1180.383
1190.0393
120.725
1200.627
1210.674
1220.544
1230.358
1240.922
1250.576
1260.164
1270.157
1280.0785
1290.126
130.00276
1300.744
1310.42
1320.599
1330.66
1340.911
1350.536
1360.277
1370.518
1380.318
1390.0404
140.477
1400.166
1410.0758
1420.268
1430.604
1440.282
1450.194
1460.32
1470.68
1480.351
1490.699
150.117
1500.404
1510.262
1520.0878
1530.878
1540.962
1550.242
1560.596
1570.648
1580.439
1590.531
1600.552
1610.45
1620.987
1630.101
1640.0745
1650.409
1660.386
1670.853
1680.807
1690.0155
170.0921
180.474
190.145
20.503
200.893
210.892
220.286
230.12
240.559
250.494
260.0113
270.492
280.294
290.199
30.158
300.542
310.622
320.0673
330.236
340.925
350.309
360.947
370.0273
380.369
390.47
40.27
400.257
410.507
420.393
430.247
440.216
450.377
460.207
470.283
480.256
490.151
50.338
500.708
510.58
520.187
530.796
540.4
550.489
560.425
570.94
580.27
590.18
60.859
600.0523
610.378
620.178
630.201
640.555
650.178
660.548
670.353
680.0108
690.611
70.0627
700.0138
710.108
720.543
730.09
740.724
750.0551
760.988
770.0692
780.0577
790.809
80.228
800.972
810.608
820.0343
830.322
840.173
850.0528
860.0511
870.407
880.524
890.267
90.736
900.0538
910.224
920.206
930.141
940.866
950.188
960.626
970.595
980.371
990.226



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: CNhs10506


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000160 (intestine)
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)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011436 (mouse intestinal mucosa- adult 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
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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