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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000079,UBERON:0000119,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000990,UBERON:0001007,UBERON:0001046,UBERON:0001062,UBERON:0001353,UBERON:0001555,UBERON:0002050,UBERON:0002367,UBERON:0002530,UBERON:0002532,UBERON:0003064,UBERON:0003101,UBERON:0003104,UBERON:0003353,UBERON:0003820,UBERON:0003929,UBERON:0003937,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004185,UBERON:0004902,UBERON:0004921,UBERON:0005153,UBERON:0005156,UBERON:0005291,UBERON:0005399,UBERON:0005423,UBERON:0005911,UBERON:0006866,UBERON:0007026,UBERON:0009142
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101019,FF:0101120
|fonse_cell_line=FF:0101019,FF:0101120
|fonse_cell_line_closure=FF:0101019,FF:0101120
|fonse_cell_line_closure=FF:0101019,FF:0101120

Revision as of 16:41, 29 March 2012


Name:prostate cancer cell line:DU145
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueprostate
dev stageNA
sexmale
age69
cell typeunclassifiable
cell lineDU145
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-penis0.104
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-lymphoma0.543
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11260

Jaspar motifP-value
MA0002.20.0102
MA0003.10.957
MA0004.10.658
MA0006.10.868
MA0007.10.813
MA0009.10.247
MA0014.10.0549
MA0017.10.41
MA0018.20.696
MA0019.10.761
MA0024.15.52591e-5
MA0025.10.969
MA0027.10.713
MA0028.11.95225e-4
MA0029.10.522
MA0030.10.109
MA0031.10.776
MA0035.20.475
MA0038.10.018
MA0039.25.31853e-4
MA0040.10.417
MA0041.10.307
MA0042.10.266
MA0043.10.4
MA0046.10.00219
MA0047.20.808
MA0048.10.153
MA0050.10.00539
MA0051.10.562
MA0052.10.0285
MA0055.11.42046e-4
MA0057.10.5
MA0058.10.637
MA0059.10.621
MA0060.11.0596e-7
MA0061.10.0136
MA0062.27.94371e-4
MA0065.20.311
MA0066.10.303
MA0067.10.827
MA0068.10.00307
MA0069.10.535
MA0070.10.921
MA0071.10.634
MA0072.10.857
MA0073.10.942
MA0074.10.874
MA0076.14.45766e-4
MA0077.10.918
MA0078.10.322
MA0079.20.723
MA0080.22.42967e-9
MA0081.10.54
MA0083.10.0737
MA0084.10.262
MA0087.10.243
MA0088.10.217
MA0090.10.363
MA0091.15.13137e-4
MA0092.10.159
MA0093.10.764
MA0099.20.312
MA0100.10.188
MA0101.10.504
MA0102.20.584
MA0103.10.00208
MA0104.20.316
MA0105.11.3659e-4
MA0106.10.731
MA0107.10.165
MA0108.20.0754
MA0111.10.684
MA0112.20.211
MA0113.10.0689
MA0114.10.425
MA0115.10.233
MA0116.10.0294
MA0117.10.322
MA0119.10.116
MA0122.10.864
MA0124.10.942
MA0125.10.204
MA0131.10.213
MA0135.10.6
MA0136.13.80474e-4
MA0137.20.217
MA0138.20.0231
MA0139.10.0324
MA0140.10.992
MA0141.10.832
MA0142.10.418
MA0143.10.0298
MA0144.10.663
MA0145.10.402
MA0146.10.688
MA0147.10.339
MA0148.10.772
MA0149.10.0266
MA0150.10.36
MA0152.10.534
MA0153.11.47146e-4
MA0154.10.00498
MA0155.10.374
MA0156.10.384
MA0157.10.286
MA0159.10.833
MA0160.10.9
MA0162.10.715
MA0163.10.17
MA0164.10.536
MA0258.10.212
MA0259.10.493



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: CNhs11260

Novel motifP-value
10.662
100.744
1000.0908
1010.237
1020.552
1030.84
1040.411
1050.818
1062.98872e-5
1070.152
1080.653
1090.249
110.387
1100.697
1110.891
1120.056
1130.0111
1140.191
1150.718
1160.777
1170.576
1180.934
1190.121
120.794
1200.459
1210.708
1220.868
1230.163
1240.0505
1250.271
1260.605
1270.539
1283.26293e-4
1290.338
130.0582
1300.615
1310.102
1320.709
1330.147
1340.737
1350.0129
1360.0153
1370.239
1380.974
1390.0061
140.642
1400.00297
1410.529
1420.632
1430.00485
1440.305
1450.392
1460.331
1470.661
1480.509
1490.0574
150.411
1500.497
1510.195
1520.492
1530.158
1540.448
1550.791
1560.972
1570.32
1580.357
1590.389
160.631
1600.5
1610.808
1620.379
1630.936
1640.401
1650.931
1660.526
1670.896
1680.232
1690.422
170.262
180.054
190.0744
20.315
200.048
210.296
220.247
230.0129
240.992
250.556
260.763
270.0964
280.598
290.805
30.291
300.991
310.205
320.0612
330.261
340.483
350.14
360.193
370.708
380.863
390.683
40.867
400.0183
410.0538
420.57
430.122
440.767
450.419
460.086
470.811
480.99
490.136
50.103
500.571
510.317
520.14
530.166
540.446
550.23
560.45
570.633
580.199
590.118
60.642
600.0517
610.276
620.0788
630.802
640.7
650.132
660.0628
670.985
680.536
690.469
70.863
700.0264
710.553
720.218
730.986
740.254
750.826
760.608
770.497
780.646
790.0914
80.385
800.0825
810.206
820.0065
830.36
840.911
850.00877
860.494
870.161
880.731
890.255
90.0694
900.399
910.0785
920.0625
930.456
940.0178
950.233
960.2
970.798
980.228
990.975



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: CNhs11260


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000079 (male reproductive system)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0001007 (digestive system)
0001046 (hindgut)
0001062 (anatomical entity)
0001353 (anal region)
0001555 (digestive tract)
0002050 (embryonic structure)
0002367 (prostate gland)
0002530 (gland)
0002532 (epiblast (generic))
0003064 (intermediate mesoderm)
0003101 (male organism)
0003104 (mesenchyme)
0003353 (epithelium of hindgut)
0003820 (prostate bud)
0003929 (gut epithelium)
0003937 (sex gland)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004902 (urogenital sinus epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006866 (terminal part of digestive tract)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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