Personal tools

FF:37-13H4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 62: Line 62:
|rna_weight_ug=
|rna_weight_ug=
|sample_age=
|sample_age=
|sample_category=developmental
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_line=

Revision as of 15:43, 26 December 2012


Name:cecum, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuececum
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
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

CNhs10467

00
10
100
1000
10000.157
1001-0.0275
1002-0.0941
1003-0.123
10040
10050
1006-0.0932
1007-0.0402
10080.819
1009-0.0572
101-0.0955
10100
1011-0.108
10120
10130.24
1014-0.0874
1015-0.329
1016-0.594
10170
10180.457
10190
1020
10200
10210
10220.457
10230
10240.0546
10250.856
10260
1027-0.048
10280
1029-0.115
103-0.0754
10300
1031-0.556
10320.595
1033-0.0752
10340
10350
1036-0.186
10370
10380.109
10390.109
1041.014
1040-0.216
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: CNhs10467

Jaspar motifP-value
MA0002.20.00189
MA0003.10.0467
MA0004.10.732
MA0006.10.216
MA0007.10.346
MA0009.10.0141
MA0014.10.617
MA0017.12.10455e-6
MA0018.20.0806
MA0019.10.957
MA0024.10.0107
MA0025.10.698
MA0027.10.223
MA0028.10.157
MA0029.10.978
MA0030.10.118
MA0031.10.0388
MA0035.20.0118
MA0038.10.568
MA0039.20.00212
MA0040.10.00846
MA0041.10.131
MA0042.10.32
MA0043.10.0362
MA0046.17.66484e-29
MA0047.25.66148e-8
MA0048.10.474
MA0050.10.329
MA0051.10.376
MA0052.10.0292
MA0055.10.252
MA0057.10.0311
MA0058.10.582
MA0059.10.712
MA0060.10.00249
MA0061.10.251
MA0062.20.109
MA0065.21.18728e-6
MA0066.10.19
MA0067.10.416
MA0068.10.00374
MA0069.10.539
MA0070.10.389
MA0071.10.346
MA0072.10.342
MA0073.10.745
MA0074.10.245
MA0076.10.105
MA0077.10.921
MA0078.10.615
MA0079.20.254
MA0080.27.61443e-5
MA0081.10.297
MA0083.10.504
MA0084.10.247
MA0087.10.557
MA0088.10.694
MA0090.10.175
MA0091.10.707
MA0092.10.409
MA0093.10.693
MA0099.21.09565e-6
MA0100.10.562
MA0101.10.966
MA0102.20.451
MA0103.13.44406e-5
MA0104.20.487
MA0105.10.0138
MA0106.10.173
MA0107.10.913
MA0108.21.08918e-9
MA0111.10.538
MA0112.21.43007e-4
MA0113.10.37
MA0114.16.04186e-7
MA0115.10.00174
MA0116.10.0399
MA0117.10.794
MA0119.10.0395
MA0122.10.962
MA0124.10.0565
MA0125.10.473
MA0131.10.266
MA0135.10.62
MA0136.10.00127
MA0137.20.986
MA0138.20.0128
MA0139.10.183
MA0140.10.614
MA0141.10.0305
MA0142.10.75
MA0143.10.223
MA0144.10.228
MA0145.10.00719
MA0146.10.569
MA0147.10.521
MA0148.16.14666e-6
MA0149.10.0285
MA0150.10.112
MA0152.10.0676
MA0153.15.69894e-22
MA0154.10.0149
MA0155.10.627
MA0156.10.156
MA0157.10.0933
MA0159.10.00231
MA0160.10.121
MA0162.10.245
MA0163.10.0235
MA0164.10.658
MA0258.10.0241
MA0259.10.278



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: CNhs10467

Novel motifP-value
10.218
100.312
1000.917
1010.517
1020.937
1030.214
1040.757
1050.0699
1060.0199
1070.0361
1080.736
1090.0799
110.291
1100.214
1110.217
1120.113
1130.704
1140.0604
1150.679
1160.428
1170.793
1180.602
1190.0589
120.555
1200.164
1210.486
1220.596
1230.721
1240.468
1250.213
1260.0607
1270.083
1280.0168
1290.287
130.0392
1300.898
1310.00626
1320.382
1330.124
1340.695
1350.994
1360.708
1370.596
1380.992
1390.00992
140.575
1400.567
1410.264
1420.394
1430.266
1440.269
1450.172
1460.141
1470.541
1480.626
1490.211
150.0982
1500.539
1510.304
1520.0754
1530.859
1540.963
1550.176
1560.597
1570.972
1580.349
1590.634
1600.265
1610.221
1620.996
1630.279
1640.478
1650.347
1660.657
1670.721
1680.68
1690.00875
170.049
180.303
190.142
20.384
200.573
210.892
220.316
230.165
240.278
250.597
260.0963
270.427
280.57
290.303
30.323
300.462
310.555
320.0691
330.414
340.61
350.758
360.381
370.111
380.409
390.519
40.103
400.226
410.255
420.676
430.21
440.343
450.309
460.219
470.326
480.258
490.172
50.0923
500.683
510.661
520.0872
530.838
540.516
550.704
560.347
570.747
580.243
590.189
60.39
600.055
610.295
620.139
630.17
640.456
650.096
660.751
670.313
680.94
690.597
70.0995
700.0252
710.187
720.531
730.111
740.53
750.282
760.4
770.118
780.0961
790.641
80.162
800.482
810.448
820.0918
830.0915
840.0244
850.0466
860.457
870.372
880.803
890.0929
90.545
900.351
910.258
920.232
930.14
940.727
950.283
960.168
970.37
980.384
990.131



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: CNhs10467


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)
0001155 (colon)
0000160 (intestine)
0001153 (caecum)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009854 (digestive tract diverticulum)
0010317 (germ layer / neural crest derived structure)
0009856 (sac)
0001555 (digestive tract)
0000059 (large intestine)
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)
0011324 (mouse cecum - 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:0001045 (midgut)
UBERON:0010316 (germ layer / neural crest)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:37-13H4&oldid=2566723"