Personal tools

FF:590-15F5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:590-15F5
|id=FF:590-15F5
|name=uterus, adult pregnant day19, biol_rep1
|name=uterus, adult pregnant day19
|sample_id=590
|sample_id=590
|rna_tube_id=590-15F5
|rna_tube_id=15F5
|rna_box=590-15F5
|rna_box=15
|rna_position=590-15F5
|rna_position=F5
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs10497,LSID648,,COMPLETED
|profile_hcage=CNhs10497,LSID648,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:59, 27 February 2012


Name:uterus, adult pregnant day19
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueuterus
dev stage19 days pregnant adult
sexfemale
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]





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

CNhs10497

00
10
100
1000
10000.0747
10010.0216
1002-0.00992
10030.0253
10040.243
10050.217
10060
1007-0.0428
10080
10090.435
101-0.0296
10100
1011-0.0328
10120
10130.352
1014-0.043
1015-0.157
1016-0.0319
10170
10180.0747
10190
1020
10200
10210
10220
10230
10240.148
10250.086
10260.109
1027-0.0147
10280
10290.108
1030.523
10300
10310.447
10320.00456
10330
10340.0747
10350
1036-0.168
10370
10380.00121
1039-0.0765
1040
10400.309
10410.194



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 no result for this sample


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: CNhs10497

Jaspar motifP-value
MA0002.20.0132
MA0003.10.0902
MA0004.10.955
MA0006.10.0817
MA0007.10.157
MA0009.10.275
MA0014.10.773
MA0017.10.247
MA0018.20.0622
MA0019.10.199
MA0024.14.64425e-5
MA0025.10.459
MA0027.10.00221
MA0028.10.0168
MA0029.10.731
MA0030.10.0256
MA0031.10.00889
MA0035.20.155
MA0038.10.75
MA0039.20.00174
MA0040.10.586
MA0041.10.677
MA0042.10.0586
MA0043.10.0172
MA0046.10.228
MA0047.20.984
MA0048.10.867
MA0050.14.3844e-7
MA0051.15.18446e-5
MA0052.10.0851
MA0055.10.3
MA0057.10.198
MA0058.10.582
MA0059.10.601
MA0060.11.18828e-9
MA0061.10.108
MA0062.20.0236
MA0065.20.896
MA0066.10.828
MA0067.10.733
MA0068.10.182
MA0069.10.925
MA0070.10.526
MA0071.10.499
MA0072.10.408
MA0073.10.533
MA0074.10.649
MA0076.10.00833
MA0077.10.00955
MA0078.10.0186
MA0079.20.00138
MA0080.25.95874e-7
MA0081.10.536
MA0083.11.94906e-9
MA0084.10.906
MA0087.10.987
MA0088.10.428
MA0090.10.00791
MA0091.10.719
MA0092.10.408
MA0093.10.903
MA0099.23.42072e-18
MA0100.10.0523
MA0101.10.283
MA0102.20.566
MA0103.10.933
MA0104.20.18
MA0105.10.762
MA0106.10.127
MA0107.10.0274
MA0108.20.00172
MA0111.10.565
MA0112.26.33075e-4
MA0113.10.624
MA0114.10.186
MA0115.10.343
MA0116.10.856
MA0117.10.662
MA0119.10.415
MA0122.10.756
MA0124.10.12
MA0125.10.189
MA0131.10.23
MA0135.10.935
MA0136.10.00177
MA0137.20.0132
MA0138.20.602
MA0139.10.436
MA0140.10.0404
MA0141.10.192
MA0142.10.456
MA0143.10.418
MA0144.18.79137e-5
MA0145.10.00277
MA0146.10.402
MA0147.10.153
MA0148.10.897
MA0149.10.539
MA0150.10.0592
MA0152.10.753
MA0153.10.812
MA0154.10.0248
MA0155.10.547
MA0156.12.49691e-4
MA0157.10.00487
MA0159.10.854
MA0160.10.232
MA0162.10.481
MA0163.10.788
MA0164.10.89
MA0258.10.0398
MA0259.10.14



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: CNhs10497

Novel motifP-value
10.937
100.581
1000.312
1010.642
1020.311
1030.486
1040.28
1050.16
1067.33772e-4
1070.00783
1080.683
1090.0512
110.902
1100.458
1110.657
1120.0187
1130.533
1140.902
1150.656
1160.314
1170.238
1180.128
1190.248
120.322
1200.272
1210.299
1220.986
1230.155
1240.667
1250.753
1260.31
1270.475
1280.0272
1290.224
130.151
1300.711
1310.195
1320.272
1330.426
1340.744
1350.456
1360.219
1370.304
1380.027
1390.1
140.479
1400.0219
1410.883
1420.278
1430.196
1440.5
1450.27
1460.402
1470.0336
1480.047
1490.00456
150.0616
1500.152
1510.652
1520.0112
1530.523
1540.941
1550.783
1560.00245
1570.668
1580.495
1590.807
1600.272
1610.262
1620.759
1630.94
1640.22
1650.146
1660.0394
1670.157
1680.0874
1690.0219
170.186
180.656
190.00893
20.0453
200.496
210.275
220.151
230.101
240.0219
250.308
260.136
270.688
280.984
290.777
30.998
300.376
310.964
320.0832
330.649
340.513
350.0566
360.097
370.0902
380.429
390.321
40.962
400.317
410.474
420.885
430.308
440.751
450.104
460.447
470.511
480.881
490.823
50.983
500.138
510.582
520.0372
530.127
540.503
550.607
560.67
570.628
580.986
590.135
60.364
600.0852
610.292
620.843
630.204
640.651
650.255
660.539
670.106
680.809
690.479
70.92
700.0144
710.723
720.443
730.0659
740.341
750.823
760.163
770.0443
780.106
790.895
80.345
800.979
810.63
820.201
830.112
840.816
850.21
860.752
870.196
880.964
890.388
90.26
900.0155
910.149
920.129
930.767
940.0875
950.453
960.259
970.426
980.694
990.324



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: CNhs10497


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)
0006834 (uterus or analog)
0007023 (adult organism)

FF: FANTOM5
NA

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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:590-15F5&oldid=418027"