Personal tools

FF:36-18H7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:36-18H7
|id=FF:36-18H7
|name=colon, adult, biol_rep1
|name=colon, adult
|sample_id=36
|sample_id=36
|rna_tube_id=36-18H7
|rna_tube_id=18H7
|rna_box=36-18H7
|rna_box=18
|rna_position=36-18H7
|rna_position=H7
|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=CNhs10468,LSID646,,COMPLETED
|profile_hcage=CNhs10468,LSID646,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:27, 27 February 2012


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





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

CNhs10468

00
10
100
1000
10000.0494
10010.0455
10020.0772
1003-0.074
10040
10050.202
1006-0.00265
1007-0.108
10082.569
1009-0.0572
101-0.111
10100.0988
1011-0.129
10120
10130.392
1014-0.0851
1015-0.242
1016-0.275
10170
10180.306
10190
1020
10200
10210
10220.179
10230
1024-0.0633
10250.296
10260
1027-0.048
10280
10290.403
103-0.0659
10300
1031-0.393
10320.565
1033-0.0648
10340.247
10350
1036-0.219
10370
10380.00864
10390.097
1040
1040-0.297
10410.0988



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: CNhs10468

Jaspar motifP-value
MA0002.27.74532e-4
MA0003.10.13
MA0004.10.864
MA0006.10.0656
MA0007.10.615
MA0009.10.327
MA0014.10.454
MA0017.12.02301e-20
MA0018.20.0464
MA0019.10.0991
MA0024.10.026
MA0025.10.936
MA0027.10.22
MA0028.10.761
MA0029.10.899
MA0030.10.974
MA0031.10.775
MA0035.27.86193e-7
MA0038.10.522
MA0039.28.15231e-4
MA0040.10.0312
MA0041.10.407
MA0042.10.457
MA0043.10.0371
MA0046.13.25867e-34
MA0047.20.00264
MA0048.10.903
MA0050.11.02218e-7
MA0051.12.3939e-5
MA0052.12.62828e-4
MA0055.10.339
MA0057.10.0625
MA0058.10.657
MA0059.10.814
MA0060.10.00102
MA0061.10.222
MA0062.20.75
MA0065.27.04638e-12
MA0066.10.0965
MA0067.10.192
MA0068.10.0101
MA0069.10.238
MA0070.10.253
MA0071.10.399
MA0072.10.954
MA0073.10.862
MA0074.10.107
MA0076.10.429
MA0077.10.702
MA0078.10.98
MA0079.20.716
MA0080.27.20261e-7
MA0081.10.793
MA0083.10.63
MA0084.10.52
MA0087.10.727
MA0088.10.503
MA0090.10.986
MA0091.10.467
MA0092.10.612
MA0093.10.779
MA0099.20.0109
MA0100.10.2
MA0101.10.649
MA0102.20.168
MA0103.11.00916e-5
MA0104.20.22
MA0105.10.108
MA0106.10.387
MA0107.10.571
MA0108.20.617
MA0111.10.91
MA0112.27.13177e-5
MA0113.10.802
MA0114.12.18648e-21
MA0115.11.40062e-11
MA0116.10.201
MA0117.10.926
MA0119.10.0717
MA0122.10.566
MA0124.10.157
MA0125.10.281
MA0131.10.379
MA0135.10.274
MA0136.11.04844e-6
MA0137.20.314
MA0138.20.293
MA0139.10.0378
MA0140.10.00591
MA0141.11.81245e-4
MA0142.10.261
MA0143.10.105
MA0144.10.033
MA0145.10.0068
MA0146.10.241
MA0147.10.385
MA0148.14.12681e-4
MA0149.10.0283
MA0150.10.329
MA0152.10.119
MA0153.12.81052e-27
MA0154.10.0108
MA0155.10.514
MA0156.10.0033
MA0157.10.682
MA0159.10.00175
MA0160.10.0161
MA0162.10.249
MA0163.10.0564
MA0164.10.901
MA0258.10.00908
MA0259.10.289



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: CNhs10468

Novel motifP-value
10.161
100.178
1000.996
1010.993
1020.922
1030.209
1040.732
1050.392
1060.0122
1070.0358
1080.712
1090.0849
110.161
1100.268
1110.0746
1120.0128
1130.901
1140.0523
1150.336
1160.24
1170.22
1180.496
1190.045
120.77
1200.434
1210.778
1220.628
1230.293
1240.913
1250.327
1260.0975
1270.159
1280.0385
1290.269
130.00466
1300.953
1310.163
1320.484
1330.732
1340.885
1350.714
1360.139
1370.48
1380.839
1390.0396
140.614
1400.301
1410.126
1420.314
1430.67
1440.223
1450.147
1460.241
1470.428
1480.258
1490.521
150.158
1500.312
1510.336
1520.0593
1530.776
1540.91
1550.339
1560.609
1570.923
1580.497
1590.216
1600.371
1610.544
1620.556
1630.21
1640.101
1650.274
1660.657
1670.95
1680.825
1690.0114
170.0973
180.253
190.0898
20.222
200.775
210.921
220.326
230.244
240.683
250.649
260.00786
270.435
280.439
290.314
30.212
300.363
310.553
320.034
330.319
340.731
350.51
360.751
370.059
380.355
390.332
40.457
400.207
410.54
420.425
430.237
440.149
450.277
460.229
470.322
480.282
490.195
50.358
500.527
510.64
520.102
530.936
540.553
550.868
560.39
570.911
580.32
590.0561
60.684
600.0424
610.216
620.27
630.156
640.563
650.134
660.649
670.403
680.067
690.798
70.11
700.0179
710.101
720.468
730.132
740.78
750.0945
760.68
770.0823
780.0688
790.115
80.141
800.455
810.645
820.0428
830.16
840.147
850.0392
860.18
870.167
880.612
890.15
90.649
900.174
910.468
920.336
930.191
940.632
950.164
960.884
970.555
980.647
990.117



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: CNhs10468


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
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001155 (colon)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)

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:36-18H7&oldid=416163"