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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0002321
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0002321
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:10696-109G3
|fonse_cell_line=FF:10696-109G3
|fonse_cell_line_closure=FF:10696-109G3
|fonse_cell_line_closure=FF:10696-109G3

Revision as of 17:13, 29 March 2012


Name:mesodermal tumor cell line:HIRS-BM
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexfemale
age16
cell typeunclassifiable
cell lineHIRS-BM
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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-penis-0.195
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-lymphoma0.0381
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs12191

Jaspar motifP-value
MA0002.20.637
MA0003.10.574
MA0004.10.269
MA0006.10.344
MA0007.10.647
MA0009.10.00945
MA0014.10.2
MA0017.10.529
MA0018.20.765
MA0019.10.284
MA0024.10.0594
MA0025.10.777
MA0027.10.927
MA0028.10.184
MA0029.10.401
MA0030.10.793
MA0031.10.0884
MA0035.20.678
MA0038.10.192
MA0039.20.432
MA0040.10.213
MA0041.10.157
MA0042.10.183
MA0043.10.278
MA0046.10.037
MA0047.20.271
MA0048.10.818
MA0050.13.60179e-4
MA0051.11.93014e-4
MA0052.10.0976
MA0055.10.47
MA0057.10.862
MA0058.10.217
MA0059.10.0298
MA0060.10.469
MA0061.10.169
MA0062.20.0202
MA0065.20.00727
MA0066.10.44
MA0067.10.78
MA0068.10.017
MA0069.10.355
MA0070.10.759
MA0071.10.311
MA0072.10.941
MA0073.10.424
MA0074.10.134
MA0076.10.319
MA0077.10.338
MA0078.10.403
MA0079.20.923
MA0080.20.0803
MA0081.10.306
MA0083.12.35478e-8
MA0084.10.127
MA0087.10.601
MA0088.10.461
MA0090.11.55531e-6
MA0091.10.203
MA0092.10.332
MA0093.10.427
MA0099.20.00875
MA0100.10.731
MA0101.10.917
MA0102.20.328
MA0103.11.56508e-4
MA0104.20.0101
MA0105.10.0136
MA0106.10.287
MA0107.10.213
MA0108.20.177
MA0111.10.597
MA0112.20.0411
MA0113.10.177
MA0114.10.0299
MA0115.10.128
MA0116.10.0267
MA0117.10.799
MA0119.10.194
MA0122.10.574
MA0124.10.731
MA0125.10.284
MA0131.10.163
MA0135.10.409
MA0136.10.04
MA0137.20.957
MA0138.20.477
MA0139.10.14
MA0140.10.742
MA0141.10.0663
MA0142.10.673
MA0143.10.78
MA0144.10.567
MA0145.10.946
MA0146.10.0122
MA0147.10.013
MA0148.10.169
MA0149.10.463
MA0150.10.734
MA0152.10.419
MA0153.10.778
MA0154.10.193
MA0155.10.213
MA0156.10.963
MA0157.10.0987
MA0159.10.0534
MA0160.10.931
MA0162.10.343
MA0163.12.37726e-5
MA0164.10.879
MA0258.10.0632
MA0259.10.0989



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: CNhs12191

Novel motifP-value
10.176
100.0551
1000.125
1010.377
1020.0912
1030.421
1040.186
1050.0449
1060.154
1070.269
1080.345
1090.121
110.324
1100.339
1110.0723
1120.668
1130.946
1140.393
1150.00524
1160.22
1170.0388
1180.192
1190.567
120.303
1200.462
1210.513
1220.865
1230.0666
1240.913
1250.694
1260.476
1270.81
1280.876
1290.158
130.0816
1300.0705
1310.186
1320.858
1330.1
1340.5
1350.471
1360.181
1370.937
1380.512
1390.8
140.986
1400.449
1410.94
1420.595
1430.409
1440.854
1450.864
1460.0854
1470.61
1480.0358
1490.374
150.181
1500.911
1510.951
1520.682
1530.323
1540.736
1550.0722
1560.61
1570.631
1580.867
1590.483
160.881
1600.122
1610.173
1620.462
1630.683
1640.034
1650.253
1660.0438
1670.112
1680.395
1690.296
170.574
180.241
190.846
20.685
200.34
210.349
220.915
230.0942
240.773
250.44
260.271
270.861
280.427
290.133
30.356
300.176
310.277
320.6
330.327
340.343
350.522
360.241
370.136
380.724
390.571
40.866
400.111
410.186
420.756
430.833
440.00796
450.162
460.372
470.11
480.152
490.926
50.202
500.758
510.936
520.804
530.72
540.487
550.125
560.881
570.776
580.38
590.936
60.503
600.738
610.152
620.283
630.955
640.47
650.818
660.227
670.804
680.547
690.946
70.998
700.431
710.0263
720.657
730.259
740.492
750.0364
760.144
770.814
780.676
790.139
80.226
800.00483
810.622
820.46
830.614
840.069
850.494
860.541
870.275
880.492
890.87
90.322
900.515
910.761
920.658
930.149
940.885
950.071
960.0757
970.102
980.0584
990.509



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: CNhs12191


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002321 (embryonic cell)

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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