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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0001008,UBERON:0001062,UBERON:0002100,UBERON:0002113,UBERON:0002417,UBERON:0003103,UBERON:0005095,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006554,UBERON:0007687
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0001008,UBERON:0001062,UBERON:0002100,UBERON:0002113,UBERON:0002417,UBERON:0003103,UBERON:0005095,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006554,UBERON:0007687
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100067
|fonse_cell_line=FF:0100067
|fonse_cell_line_closure=FF:0100067
|fonse_cell_line_closure=FF:0100067

Revision as of 16:56, 29 March 2012


Name:leiomyoblastoma cell line:G-402
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexfemale
age9 months
cell typeunclassifiable
cell lineG-402
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.083
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.467
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs11848

Jaspar motifP-value
MA0002.20.0804
MA0003.10.23
MA0004.10.955
MA0006.10.351
MA0007.10.613
MA0009.10.11
MA0014.10.346
MA0017.10.135
MA0018.20.0239
MA0019.10.0822
MA0024.14.83008e-5
MA0025.10.375
MA0027.10.0826
MA0028.10.0205
MA0029.10.724
MA0030.10.0414
MA0031.10.0233
MA0035.20.241
MA0038.10.435
MA0039.20.0283
MA0040.10.199
MA0041.10.542
MA0042.10.615
MA0043.10.065
MA0046.10.102
MA0047.20.478
MA0048.10.0459
MA0050.11.77063e-7
MA0051.11.22213e-6
MA0052.10.874
MA0055.11.30614e-5
MA0057.10.933
MA0058.10.425
MA0059.10.795
MA0060.11.00131e-4
MA0061.10.00305
MA0062.20.263
MA0065.20.498
MA0066.10.813
MA0067.10.605
MA0068.10.114
MA0069.10.672
MA0070.10.177
MA0071.10.369
MA0072.10.81
MA0073.10.686
MA0074.10.138
MA0076.10.00654
MA0077.10.122
MA0078.10.142
MA0079.20.372
MA0080.21.63846e-13
MA0081.10.0403
MA0083.10.302
MA0084.10.138
MA0087.10.213
MA0088.15.45341e-5
MA0090.10.837
MA0091.10.174
MA0092.10.58
MA0093.10.854
MA0099.21.79774e-6
MA0100.10.499
MA0101.10.159
MA0102.20.141
MA0103.10.828
MA0104.20.0301
MA0105.10.0276
MA0106.10.0309
MA0107.10.00896
MA0108.20.00388
MA0111.10.897
MA0112.20.151
MA0113.10.053
MA0114.10.187
MA0115.10.876
MA0116.10.137
MA0117.10.526
MA0119.10.36
MA0122.10.9
MA0124.10.669
MA0125.10.699
MA0131.10.509
MA0135.10.0178
MA0136.14.20819e-11
MA0137.20.036
MA0138.20.595
MA0139.10.583
MA0140.10.361
MA0141.10.326
MA0142.10.0769
MA0143.10.349
MA0144.10.00532
MA0145.10.237
MA0146.10.00421
MA0147.10.00134
MA0148.10.256
MA0149.10.33
MA0150.10.0189
MA0152.10.513
MA0153.10.0981
MA0154.10.0291
MA0155.10.756
MA0156.11.07929e-5
MA0157.10.00146
MA0159.10.191
MA0160.10.532
MA0162.10.287
MA0163.10.508
MA0164.10.482
MA0258.10.64
MA0259.10.0439



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: CNhs11848

Novel motifP-value
10.338
100.33
1000.0639
1010.647
1020.998
1030.222
1040.504
1050.834
1063.09753e-6
1070.0152
1080.989
1090.0133
110.366
1100.208
1110.536
1120.34
1130.0145
1140.493
1150.932
1160.584
1170.11
1180.837
1190.134
120.434
1200.717
1210.0811
1220.815
1230.218
1240.838
1250.931
1260.837
1270.583
1280.00116
1290.702
130.0359
1300.959
1310.351
1320.542
1330.00657
1340.356
1350.125
1360.0497
1370.622
1380.513
1390.151
140.395
1400.24
1410.538
1420.807
1430.0619
1440.697
1450.492
1460.295
1470.408
1480.545
1490.0339
150.498
1500.0915
1510.265
1520.975
1530.118
1540.967
1550.316
1560.786
1570.643
1580.331
1590.251
160.648
1600.928
1610.644
1620.153
1630.0499
1640.972
1650.315
1660.163
1670.761
1680.0146
1690.721
170.399
180.206
190.421
20.0938
200.123
210.885
220.936
230.00211
240.956
250.633
260.564
270.243
280.966
290.475
30.504
300.302
310.27
320.877
330.974
340.477
350.597
360.0774
370.815
380.484
390.389
40.912
400.00932
410.0906
420.0875
430.247
440.481
450.0512
460.681
470.0347
480.182
490.983
50.184
500.9
510.945
520.123
530.575
540.595
550.737
560.687
570.383
580.0919
590.0937
60.895
600.0592
610.361
620.202
630.961
640.536
650.0291
660.0563
670.927
680.116
690.468
70.372
700.767
710.918
720.138
730.442
740.161
750.0847
760.809
770.477
780.933
790.18
80.112
800.0228
810.617
820.711
830.706
840.982
850.0406
860.581
870.105
880.0904
890.651
90.281
900.944
910.0494
920.0604
930.753
940.984
950.00165
960.855
970.823
980.408
990.601



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: CNhs11848


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

DOID: Disease
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0001008 (renal system)
0001062 (anatomical entity)
0002100 (trunk)
0002113 (kidney)
0002417 (abdominal segment of trunk)
0003103 (compound organ)
0005095 (kidney rudiment)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006554 (urinary system structure)
0007687 (kidney field)

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

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