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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000153,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001004,UBERON:0001062,UBERON:0001764,UBERON:0001825,UBERON:0002553
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000153,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0001004,UBERON:0001062,UBERON:0001764,UBERON:0001825,UBERON:0002553
|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:10414-106B9
|fonse_cell_line=FF:10414-106B9
|fonse_cell_line_closure=FF:10414-106B9
|fonse_cell_line_closure=FF:10414-106B9

Revision as of 16:31, 29 March 2012


Name:maxillary sinus tumor cell line:HSQ-89
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesinus
dev stage74 year old adult
sexmale
age74
cell typeunclassifiable
cell lineHSQ-89
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-penis0
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-lymphoma0.215
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
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: CNhs10732

Jaspar motifP-value
MA0002.23.23725e-4
MA0003.10.282
MA0004.10.191
MA0006.10.61
MA0007.10.32
MA0009.10.284
MA0014.10.358
MA0017.10.118
MA0018.20.0528
MA0019.10.154
MA0024.10.0189
MA0025.10.00972
MA0027.10.803
MA0028.10.00196
MA0029.10.867
MA0030.10.00535
MA0031.10.098
MA0035.20.571
MA0038.10.00586
MA0039.20.0923
MA0040.10.139
MA0041.10.902
MA0042.10.58
MA0043.10.00119
MA0046.10.471
MA0047.23.78018e-4
MA0048.10.609
MA0050.15.0188e-5
MA0051.10.003
MA0052.10.0679
MA0055.10.413
MA0057.10.727
MA0058.10.173
MA0059.10.717
MA0060.13.3953e-7
MA0061.10.00176
MA0062.24.04956e-4
MA0065.20.0335
MA0066.10.0255
MA0067.10.811
MA0068.10.165
MA0069.10.366
MA0070.10.0907
MA0071.10.645
MA0072.10.891
MA0073.10.396
MA0074.10.145
MA0076.11.42713e-4
MA0077.10.0172
MA0078.10.376
MA0079.20.171
MA0080.21.00388e-7
MA0081.10.027
MA0083.14.29387e-6
MA0084.10.671
MA0087.10.947
MA0088.10.789
MA0090.10.143
MA0091.10.00293
MA0092.10.0678
MA0093.10.135
MA0099.22.46443e-4
MA0100.10.47
MA0101.10.034
MA0102.20.829
MA0103.13.13679e-4
MA0104.20.221
MA0105.11.91468e-6
MA0106.10.807
MA0107.10.0126
MA0108.20.252
MA0111.10.951
MA0112.22.68828e-4
MA0113.10.0553
MA0114.10.465
MA0115.10.357
MA0116.11.12936e-4
MA0117.10.96
MA0119.10.0911
MA0122.10.394
MA0124.10.753
MA0125.10.421
MA0131.10.41
MA0135.10.977
MA0136.10.0015
MA0137.20.111
MA0138.20.235
MA0139.10.666
MA0140.10.183
MA0141.10.13
MA0142.10.395
MA0143.10.127
MA0144.10.101
MA0145.10.444
MA0146.10.596
MA0147.10.255
MA0148.10.00498
MA0149.10.78
MA0150.10.585
MA0152.10.555
MA0153.10.869
MA0154.10.00193
MA0155.10.0615
MA0156.10.245
MA0157.10.635
MA0159.10.503
MA0160.10.345
MA0162.10.156
MA0163.11.2592e-6
MA0164.10.159
MA0258.10.0234
MA0259.10.174



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: CNhs10732

Novel motifP-value
10.36
100.135
1000.917
1010.709
1020.777
1030.0611
1040.762
1050.936
1060.00109
1070.0187
1080.98
1090.257
110.0486
1100.264
1110.156
1120.0339
1130.25
1140.0357
1150.363
1160.195
1170.507
1180.525
1190.0926
120.764
1200.856
1210.762
1220.676
1230.692
1240.175
1250.44
1260.519
1270.521
1280.033
1290.53
130.843
1300.638
1310.222
1320.661
1330.0718
1340.785
1350.0166
1360.443
1370.306
1380.424
1390.06
140.897
1400.116
1410.654
1420.407
1430.00579
1440.0328
1450.0546
1460.632
1470.171
1480.311
1490.0511
150.263
1500.331
1510.426
1520.297
1530.711
1540.58
1550.375
1560.554
1570.275
1580.897
1590.56
160.198
1600.0607
1610.326
1620.111
1630.797
1640.788
1650.148
1660.329
1670.841
1680.13
1690.0215
170.19
180.163
190.0824
20.412
200.587
210.149
220.184
230.0402
240.882
250.622
260.157
270.233
280.912
290.712
30.107
300.65
310.573
320.00281
330.246
340.283
350.144
360.763
370.25
380.316
390.203
40.944
400.854
410.113
420.405
430.108
440.134
450.525
460.0298
470.538
480.351
490.15
50.231
500.879
510.382
520.293
530.593
540.311
550.516
560.583
570.636
580.345
590.0236
60.519
600.0442
610.683
620.0669
630.222
640.459
650.0306
660.285
670.689
680.00789
690.22
70.728
700.146
710.108
720.388
730.239
740.0794
750.509
760.978
770.0966
780.727
790.06
80.0883
800.115
810.134
820.0478
830.473
840.546
850.00753
860.64
870.832
880.78
890.0683
90.0872
900.448
910.0815
920.037
930.663
940.0755
950.58
960.0677
970.623
980.274
990.544



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: CNhs10732


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
0000033 (head)
0000061 (anatomical structure)
0000153 (anterior region of body)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0001004 (respiratory system)
0001062 (anatomical entity)
0001764 (maxillary sinus)
0001825 (paranasal sinus)
0002553 (anatomical cavity)

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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