Personal tools

FF:1525-43A6: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008801
|DRA_sample_Accession=CAGE@SAMD00005320
|accession_numbers=CAGE;DRX008938;DRR009812;DRZ001237;DRZ002620
|accession_numbers=CAGE;DRX008938;DRR009812;DRZ001237;DRZ002620
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000981,UBERON:0001474,UBERON:0000479,UBERON:0011216,UBERON:0000062,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0002472,UBERON:0008784,UBERON:0001062,UBERON:0000480,UBERON:0006058,UBERON:0003608,UBERON:0003826,UBERON:0008202,UBERON:0000075,UBERON:0004381,UBERON:0007273,UBERON:0004765,UBERON:0010912,UBERON:0004708,UBERON:0002101,UBERON:0004709,UBERON:0002513,UBERON:0004375,UBERON:0010740,UBERON:0002529,UBERON:0010363,UBERON:0010538,UBERON:0002428,UBERON:0010742,UBERON:0002495,UBERON:0003464,UBERON:0003606,UBERON:0005893,UBERON:0010317,UBERON:0010712,UBERON:0010758,UBERON:0010707,UBERON:0002204,UBERON:0001434,UBERON:0000978,UBERON:0002103,UBERON:0000376,UBERON:0001441,UBERON:0011249,UBERON:0000154,UBERON:0010709,UBERON:0002091,UBERON:0004288
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000981,UBERON:0001474,UBERON:0000479,UBERON:0011216,UBERON:0000062,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0002472,UBERON:0008784,UBERON:0001062,UBERON:0000480,UBERON:0006058,UBERON:0003608,UBERON:0003826,UBERON:0008202,UBERON:0000075,UBERON:0004381,UBERON:0007273,UBERON:0004765,UBERON:0010912,UBERON:0004708,UBERON:0002101,UBERON:0004709,UBERON:0002513,UBERON:0004375,UBERON:0010740,UBERON:0002529,UBERON:0010363,UBERON:0010538,UBERON:0002428,UBERON:0010742,UBERON:0002495,UBERON:0003464,UBERON:0003606,UBERON:0005893,UBERON:0010317,UBERON:0010712,UBERON:0010758,UBERON:0010707,UBERON:0002204,UBERON:0001434,UBERON:0000978,UBERON:0002103,UBERON:0000376,UBERON:0001441,UBERON:0011249,UBERON:0000154,UBERON:0010709,UBERON:0002091,UBERON:0004288

Revision as of 21:43, 31 July 2014


Name:bone (os femoris), neonate N16
Species:Mouse (Mus musculus)
Library ID:CNhs11225
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuebone (os femoris)
dev stage16 days neonate
sexmixture
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  SAMD00005320
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11225 CAGE DRX008938 DRR009812
Accession ID Mm9

Library idBAMCTSS
CNhs11225 DRZ001237 DRZ002620
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

CNhs11225

00
10
100
1000
10000.5
10010.477
1002-0.0184
10030.202
10040
10050.159
10060.471
10070.0255
10080
10090.0308
101-0.0109
10100
10110
10120.275
1013-0.125
10140.0867
1015-0.117
1016-0.0563
10170
10180
10190
1020
10200
10210.159
10220.488
10230
10240.159
10250
10260
10270.0867
10280
10290.436
1030.942
10300.843
10310.0391
10325.473114e-4
10330
10340
10350.159
10360.0137
10370
1038-0.0249
10390.204
1040
10400.0629
10410.159



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: CNhs11225

Jaspar motifP-value
MA0002.20.141
MA0003.10.0829
MA0004.10.31
MA0006.10.0721
MA0007.10.901
MA0009.10.456
MA0014.10.521
MA0017.10.607
MA0018.21.78397e-4
MA0019.10.0666
MA0024.10.188
MA0025.10.134
MA0027.10.227
MA0028.10.034
MA0029.10.957
MA0030.10.594
MA0031.10.386
MA0035.20.0475
MA0038.10.598
MA0039.20.748
MA0040.10.639
MA0041.10.0825
MA0042.10.993
MA0043.10.00132
MA0046.16.0018e-17
MA0047.20.311
MA0048.10.75
MA0050.10.928
MA0051.10.826
MA0052.11.32842e-23
MA0055.10.304
MA0057.10.421
MA0058.10.141
MA0059.10.16
MA0060.10.14
MA0061.10.0828
MA0062.20.00917
MA0065.20.26
MA0066.10.142
MA0067.10.282
MA0068.10.107
MA0069.10.0816
MA0070.10.54
MA0071.10.753
MA0072.10.4
MA0073.10.891
MA0074.10.836
MA0076.10.008
MA0077.10.125
MA0078.10.225
MA0079.20.802
MA0080.20.0341
MA0081.10.144
MA0083.10.00131
MA0084.10.547
MA0087.10.179
MA0088.10.97
MA0090.10.867
MA0091.10.0438
MA0092.10.423
MA0093.10.279
MA0099.20.645
MA0100.10.771
MA0101.10.854
MA0102.20.516
MA0103.10.015
MA0104.20.0826
MA0105.10.0186
MA0106.10.471
MA0107.10.576
MA0108.20.0539
MA0111.10.884
MA0112.21.99088e-7
MA0113.10.499
MA0114.10.293
MA0115.10.171
MA0116.10.014
MA0117.10.943
MA0119.10.136
MA0122.10.753
MA0124.10.644
MA0125.10.417
MA0131.10.847
MA0135.10.148
MA0136.10.967
MA0137.20.00154
MA0138.20.419
MA0139.10.776
MA0140.13.68197e-13
MA0141.10.0179
MA0142.10.714
MA0143.10.16
MA0144.10.26
MA0145.10.161
MA0146.10.289
MA0147.10.206
MA0148.10.545
MA0149.10.254
MA0150.10.107
MA0152.10.123
MA0153.14.31841e-12
MA0154.10.00197
MA0155.10.331
MA0156.10.931
MA0157.10.327
MA0159.10.145
MA0160.10.189
MA0162.10.198
MA0163.13.88134e-4
MA0164.10.805
MA0258.11.73013e-4
MA0259.10.355



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: CNhs11225

Novel motifP-value
10.179
100.202
1000.659
1010.911
1020.869
1030.267
1040.691
1050.246
1060.0447
1070.118
1080.99
1090.051
110.298
1100.161
1110.615
1120.418
1130.989
1140.435
1150.829
1160.672
1170.212
1180.501
1190.158
120.316
1200.419
1210.584
1220.893
1230.7
1240.0948
1250.0912
1260.285
1270.0792
1280.0924
1290.892
130.00959
1300.755
1310.858
1320.768
1330.623
1340.503
1350.777
1360.448
1370.0679
1380.309
1390.469
140.293
1400.0996
1410.701
1420.239
1430.733
1440.0391
1450.353
1460.991
1470.762
1480.417
1490.877
150.321
1500.239
1510.185
1520.178
1530.819
1540.616
1550.356
1563.49556e-26
1570.886
1580.101
1590.0141
1600.0835
1610.992
1620.696
1630.451
1640.406
1650.117
1660.899
1670.928
1680.372
1695.92162e-4
170.218
180.802
190.0309
20.578
200.369
210.35
220.159
230.581
240.95
250.577
260.0112
270.818
280.608
290.269
30.13
300.684
310.349
320.00116
330.602
340.171
350.611
360.411
370.0563
380.982
390.282
40.623
400.482
410.588
420.592
430.207
440.802
450.41
460.163
470.768
480.733
490.304
50.0226
500.284
510.685
520.29
530.563
540.528
550.854
560.409
570.306
580.389
590.0152
60.766
600.104
610.672
620.163
630.117
640.762
650.867
660.362
670.145
680.277
690.131
70.0542
700.424
710.0404
720.976
730.13
740.777
750.382
760.947
770.623
780.00798
790.885
80.248
800.0728
810.355
820.414
830.474
840.946
850.0797
860.597
870.00655
880.375
890.339
90.191
900.706
910.0401
920.598
930.302
940.133
950.105
960.188
970.435
980.629
990.837



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: CNhs11225


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)
0000981 (femur)
0001474 (bone element)
0000479 (tissue)
0011216 (organ system subdivision)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0002472 (stylopod)
0008784 (lower limb segment)
0001062 (anatomical entity)
0000480 (anatomical group)
0006058 (multi-limb segment region)
0003608 (hindlimb long bone)
0003826 (upper leg bone)
0008202 (bone of hip region)
0000075 (subdivision of skeletal system)
0004381 (skeleton of limb)
0007273 (pelvic appendage skeleton)
0004765 (skeletal element)
0010912 (subdivision of skeleton)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0002513 (endochondral bone)
0004375 (bone of free limb or fin)
0010740 (bone of appendage girdle complex)
0002529 (limb segment)
0010363 (endochondral element)
0010538 (paired limb/fin segment)
0002428 (limb bone)
0010742 (bone of pelvic complex)
0002495 (long bone)
0003464 (hindlimb bone)
0003606 (limb long bone)
0005893 (leg bone)
0010317 (germ layer / neural crest derived structure)
0010712 (limb skeleton subdivision)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0000978 (leg)
0002103 (hindlimb)
0000376 (hindlimb stylopod)
0001441 (hindlimb skeleton)
0011249 (appendicular skeletal system)
0000154 (posterior region of body)
0010709 (pelvic complex)
0002091 (appendicular skeleton)
0004288 (skeleton)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000306 (mouse neonate N16 sample)
0011462 (mouse bone- os femoris - neonate N16 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:0006603 (presumptive mesoderm)
UBERON:0003104 (mesenchyme)
UBERON:0005866 (pre-cartilage condensation)
UBERON:0006234 (femur pre-cartilage condensation)
UBERON:0010316 (germ layer / neural crest)
UBERON:0010882 (limb bone pre-cartilage condensation)
UBERON:0010886 (hindlimb bone pre-cartilage condensation)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1525-43A6&oldid=3271552"