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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|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:0100400
|fonse_cell_line=FF:0100400
|fonse_cell_line_closure=FF:0100400
|fonse_cell_line_closure=FF:0100400

Revision as of 16:57, 29 March 2012


Name:pagetoid sarcoma cell line:Hs 925.T
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueskin
dev stageNA
sexmale
age58
cell typeunclassifiable
cell lineHs 925.T
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-penis0.398
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-lymphoma0.318
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs11856

Jaspar motifP-value
MA0002.20.711
MA0003.10.0633
MA0004.10.464
MA0006.10.379
MA0007.10.657
MA0009.10.247
MA0014.10.712
MA0017.10.00785
MA0018.20.337
MA0019.10.873
MA0024.10.373
MA0025.10.622
MA0027.10.887
MA0028.16.60868e-5
MA0029.10.141
MA0030.10.00653
MA0031.10.109
MA0035.20.134
MA0038.10.00121
MA0039.20.79
MA0040.10.0925
MA0041.10.229
MA0042.10.273
MA0043.10.516
MA0046.10.00356
MA0047.20.262
MA0048.10.0157
MA0050.10.0303
MA0051.10.266
MA0052.10.226
MA0055.10.0682
MA0057.10.508
MA0058.10.803
MA0059.10.173
MA0060.12.02139e-12
MA0061.10.475
MA0062.28.90253e-4
MA0065.20.0375
MA0066.10.438
MA0067.10.358
MA0068.10.28
MA0069.10.0323
MA0070.10.856
MA0071.10.975
MA0072.10.621
MA0073.10.354
MA0074.10.669
MA0076.13.94537e-6
MA0077.10.821
MA0078.10.368
MA0079.20.427
MA0080.22.00247e-9
MA0081.10.0507
MA0083.10.143
MA0084.10.448
MA0087.10.147
MA0088.10.135
MA0090.10.371
MA0091.10.0167
MA0092.10.654
MA0093.10.425
MA0099.20.00881
MA0100.10.14
MA0101.10.445
MA0102.20.0155
MA0103.10.00932
MA0104.20.0887
MA0105.10.224
MA0106.10.986
MA0107.10.995
MA0108.20.946
MA0111.10.464
MA0112.20.0772
MA0113.10.328
MA0114.10.0212
MA0115.10.522
MA0116.10.0573
MA0117.10.29
MA0119.10.612
MA0122.10.834
MA0124.10.893
MA0125.10.122
MA0131.10.122
MA0135.10.0215
MA0136.15.16327e-8
MA0137.20.703
MA0138.20.0346
MA0139.10.311
MA0140.10.82
MA0141.10.507
MA0142.10.151
MA0143.10.292
MA0144.10.862
MA0145.10.156
MA0146.10.104
MA0147.10.0211
MA0148.10.6
MA0149.10.302
MA0150.10.498
MA0152.10.333
MA0153.10.319
MA0154.10.00313
MA0155.10.175
MA0156.10.0437
MA0157.10.289
MA0159.10.552
MA0160.10.171
MA0162.10.483
MA0163.10.559
MA0164.10.236
MA0258.10.263
MA0259.19.03572e-4



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: CNhs11856

Novel motifP-value
10.39
100.805
1000.298
1010.4
1020.649
1030.671
1040.725
1050.0401
1060.0959
1070.665
1080.221
1090.442
110.822
1100.963
1110.204
1120.468
1130.105
1140.997
1150.669
1160.542
1170.988
1180.418
1190.761
120.258
1200.989
1210.607
1220.383
1230.34
1240.272
1250.348
1260.621
1270.619
1280.282
1290.398
130.801
1300.276
1310.0524
1320.605
1330.658
1340.772
1350.00784
1360.0878
1370.0969
1380.691
1390.945
140.0818
1400.0665
1410.135
1420.757
1430.296
1440.698
1450.964
1460.286
1470.446
1480.14
1490.228
150.983
1500.238
1510.93
1520.182
1530.908
1540.249
1550.427
1560.998
1570.715
1580.204
1590.108
160.696
1600.155
1610.745
1620.315
1630.852
1640.93
1650.464
1660.626
1670.305
1680.193
1690.0394
170.486
180.454
190.285
20.7
200.169
210.542
220.0341
230.558
240.623
250.51
260.42
270.0213
280.844
290.347
30.563
300.37
310.656
326.28583e-4
330.557
340.195
350.772
360.834
370.548
380.512
390.538
40.182
400.735
410.0434
420.776
430.254
440.694
450.392
460.916
470.978
480.665
490.628
50.176
500.877
510.548
520.154
530.714
540.899
550.666
560.851
570.999
580.195
590.362
60.344
600.277
610.858
620.367
630.886
640.703
650.422
666.48234e-5
670.091
680.949
690.817
70.121
700.241
710.821
720.143
730.396
740.914
750.432
760.762
770.563
780.589
790.515
80.998
800.0225
810.657
820.472
830.471
840.818
850.0316
860.845
870.117
880.636
890.172
90.00704
900.905
910.0917
920.833
930.992
940.759
950.996
960.656
970.416
980.0132
990.418



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: CNhs11856


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
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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