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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000076,UBERON:0000119,UBERON:0000310,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001048,UBERON:0001062,UBERON:0001443,UBERON:0001911,UBERON:0002050,UBERON:0002330,UBERON:0002365,UBERON:0002530,UBERON:0002532,UBERON:0003100,UBERON:0004121,UBERON:0005085,UBERON:0005153,UBERON:0005291,UBERON:0005311,UBERON:0005333,UBERON:0005423,UBERON:0005482,UBERON:0008425
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000076,UBERON:0000119,UBERON:0000310,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001048,UBERON:0001062,UBERON:0001443,UBERON:0001911,UBERON:0002050,UBERON:0002330,UBERON:0002365,UBERON:0002530,UBERON:0002532,UBERON:0003100,UBERON:0004121,UBERON:0005085,UBERON:0005153,UBERON:0005291,UBERON:0005311,UBERON:0005333,UBERON:0005423,UBERON:0005482,UBERON:0008425
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|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:0100816,FF:0101120
|fonse_cell_line=FF:0100816,FF:0101120
|fonse_cell_line_closure=FF:0100816,FF:0101120
|fonse_cell_line_closure=FF:0100816,FF:0101120

Revision as of 16:31, 29 March 2012


Name:breast carcinoma cell line:MDA-MB-453
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebreast
dev stageNA
sexfemale
ageunknown
cell typeunclassifiable
cell lineMDA-MB-453
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-0.0332
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0.842
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs10736

Jaspar motifP-value
MA0002.20.00873
MA0003.10.271
MA0004.10.679
MA0006.10.462
MA0007.10.533
MA0009.10.964
MA0014.10.0396
MA0017.10.0971
MA0018.20.992
MA0019.10.983
MA0024.16.86553e-4
MA0025.10.0998
MA0027.10.745
MA0028.13.45304e-4
MA0029.10.129
MA0030.10.247
MA0031.10.0831
MA0035.20.656
MA0038.10.00517
MA0039.20.00801
MA0040.10.77
MA0041.10.53
MA0042.10.577
MA0043.10.673
MA0046.10.0316
MA0047.23.79081e-5
MA0048.10.531
MA0050.16.25861e-7
MA0051.10.004
MA0052.10.125
MA0055.10.00229
MA0057.10.938
MA0058.10.546
MA0059.10.54
MA0060.11.36706e-17
MA0061.19.25525e-5
MA0062.20.00244
MA0065.20.617
MA0066.10.152
MA0067.10.607
MA0068.10.626
MA0069.10.62
MA0070.10.163
MA0071.10.792
MA0072.10.0166
MA0073.10.864
MA0074.10.308
MA0076.11.92676e-4
MA0077.10.666
MA0078.10.831
MA0079.20.198
MA0080.22.69579e-7
MA0081.10.0179
MA0083.10.0098
MA0084.10.145
MA0087.10.854
MA0088.10.881
MA0090.10.959
MA0091.10.0732
MA0092.10.13
MA0093.10.603
MA0099.24.2499e-8
MA0100.10.174
MA0101.10.00741
MA0102.20.155
MA0103.12.64162e-7
MA0104.20.106
MA0105.18.54877e-6
MA0106.10.127
MA0107.10.00212
MA0108.20.664
MA0111.10.791
MA0112.20.148
MA0113.10.939
MA0114.10.899
MA0115.10.836
MA0116.10.0193
MA0117.10.691
MA0119.10.995
MA0122.10.74
MA0124.10.343
MA0125.10.0139
MA0131.10.0329
MA0135.10.36
MA0136.10.00112
MA0137.20.262
MA0138.20.129
MA0139.10.678
MA0140.10.8
MA0141.10.331
MA0142.10.509
MA0143.10.07
MA0144.10.222
MA0145.10.686
MA0146.10.222
MA0147.10.0845
MA0148.12.41986e-5
MA0149.10.699
MA0150.10.00145
MA0152.10.871
MA0153.10.772
MA0154.10.0217
MA0155.10.101
MA0156.10.0782
MA0157.10.791
MA0159.10.671
MA0160.10.984
MA0162.10.283
MA0163.10.00441
MA0164.10.431
MA0258.10.506
MA0259.10.0431



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: CNhs10736

Novel motifP-value
10.77
100.471
1000.679
1010.392
1020.919
1030.072
1040.472
1050.949
1060.00551
1070.0446
1080.975
1090.739
110.374
1100.65
1110.528
1120.146
1130.0462
1140.231
1150.205
1160.23
1170.246
1180.28
1190.959
120.721
1200.653
1210.213
1220.0881
1230.277
1240.097
1250.243
1260.969
1270.775
1280.0255
1290.887
130.113
1300.357
1310.164
1320.221
1330.277
1340.818
1350.147
1360.0977
1370.317
1380.225
1390.88
140.757
1400.144
1410.911
1420.817
1430.168
1440.0441
1450.189
1460.725
1470.334
1480.223
1490.114
150.704
1500.948
1510.287
1520.0454
1530.705
1540.882
1550.135
1560.17
1570.821
1580.971
1590.903
160.189
1600.23
1610.824
1620.761
1630.311
1640.875
1650.649
1660.0119
1670.944
1680.00152
1690.675
170.999
180.0347
190.211
20.253
200.259
210.415
220.515
230.0523
240.571
250.608
260.811
270.78
280.603
290.261
30.244
300.547
310.337
320.0588
330.93
340.134
350.254
360.529
370.0785
380.573
390.746
40.582
400.634
410.0741
420.761
430.0918
440.183
450.966
460.244
470.904
480.892
490.536
50.373
500.889
510.685
520.222
530.725
540.672
550.473
560.494
570.858
580.435
590.0158
60.313
600.077
610.614
620.115
630.937
640.99
650.258
660.00362
670.224
680.0612
690.515
70.874
700.255
710.449
720.341
730.224
740.18
750.203
760.893
770.237
780.57
790.0132
80.122
800.193
810.101
820.0547
830.469
840.912
850.0517
860.658
870.168
880.614
890.268
90.106
900.162
910.179
920.0797
930.411
940.318
950.315
960.0784
970.622
980.253
990.692



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: CNhs10736


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
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
1612 (breast cancer)
162 (cancer)
305 (carcinoma)
4 (disease)
5093 (thoracic cancer)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000076 (external ectoderm)
0000119 (cell layer)
0000310 (breast)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001048 (primordium)
0001062 (anatomical entity)
0001443 (chest)
0001911 (mammary gland)
0002050 (embryonic structure)
0002330 (exocrine system)
0002365 (exocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0003100 (female organism)
0004121 (ectoderm-derived structure)
0005085 (ectodermal placode)
0005153 (epithelial bud)
0005291 (embryonic tissue)
0005311 (mammary placode)
0005333 (mammary bud)
0005423 (developing anatomical structure)
0008425 (mammary ridge)

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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