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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000310,UBERON:0000465,UBERON:0000468,UBERON:0000475,UBERON:0000915,UBERON:0001062,UBERON:0001443,UBERON:0005482
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000310,UBERON:0000465,UBERON:0000468,UBERON:0000475,UBERON:0000915,UBERON:0001062,UBERON:0001443,UBERON:0005482
|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 17:02, 29 March 2012


Name:breast carcinoma cell line:MCF7
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
age69
cell typeunclassifiable
cell lineMCF7
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-penis0.127
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-lymphoma0.205
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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: CNhs11943

Jaspar motifP-value
MA0002.20.00977
MA0003.10.252
MA0004.10.0111
MA0006.10.871
MA0007.10.81
MA0009.10.876
MA0014.10.223
MA0017.10.0544
MA0018.20.775
MA0019.10.267
MA0024.10.00553
MA0025.10.919
MA0027.10.953
MA0028.10.181
MA0029.10.332
MA0030.10.162
MA0031.10.422
MA0035.20.914
MA0038.10.0186
MA0039.20.352
MA0040.10.259
MA0041.10.506
MA0042.10.615
MA0043.10.251
MA0046.10.313
MA0047.20.00838
MA0048.10.816
MA0050.16.33121e-12
MA0051.11.70307e-6
MA0052.10.0117
MA0055.10.436
MA0057.10.659
MA0058.10.0232
MA0059.10.313
MA0060.11.43175e-7
MA0061.18.60468e-5
MA0062.20.292
MA0065.20.321
MA0066.10.337
MA0067.10.269
MA0068.10.822
MA0069.10.825
MA0070.10.861
MA0071.10.394
MA0072.10.822
MA0073.10.938
MA0074.10.917
MA0076.10.0347
MA0077.10.945
MA0078.10.279
MA0079.20.44
MA0080.25.52519e-10
MA0081.10.0126
MA0083.10.0128
MA0084.10.528
MA0087.10.833
MA0088.10.295
MA0090.10.674
MA0091.10.0521
MA0092.10.273
MA0093.10.0165
MA0099.21.01243e-6
MA0100.10.75
MA0101.10.00401
MA0102.20.0142
MA0103.15.93851e-7
MA0104.20.296
MA0105.11.08241e-5
MA0106.10.366
MA0107.11.80688e-4
MA0108.20.00894
MA0111.10.658
MA0112.20.133
MA0113.10.361
MA0114.10.334
MA0115.10.849
MA0116.10.00175
MA0117.10.423
MA0119.10.472
MA0122.10.835
MA0124.10.311
MA0125.10.0682
MA0131.10.154
MA0135.10.244
MA0136.12.43013e-7
MA0137.20.0618
MA0138.20.21
MA0139.10.562
MA0140.10.915
MA0141.10.527
MA0142.10.237
MA0143.10.52
MA0144.10.0726
MA0145.10.689
MA0146.10.895
MA0147.10.257
MA0148.10.0573
MA0149.10.286
MA0150.10.00127
MA0152.10.861
MA0153.10.673
MA0154.10.00957
MA0155.10.0993
MA0156.12.83618e-4
MA0157.10.961
MA0159.10.648
MA0160.10.693
MA0162.10.164
MA0163.14.09401e-5
MA0164.10.401
MA0258.10.761
MA0259.10.106



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: CNhs11943

Novel motifP-value
10.73
100.497
1000.946
1010.35
1020.482
1030.113
1040.485
1050.0744
1060.09
1070.438
1080.524
1090.883
110.296
1100.627
1110.802
1120.511
1130.173
1140.153
1150.31
1160.259
1170.708
1180.252
1190.506
120.403
1200.861
1210.225
1220.284
1230.136
1240.0875
1250.613
1260.759
1270.984
1280.217
1290.524
130.745
1300.485
1310.228
1320.958
1330.00212
1340.382
1350.232
1360.0213
1370.152
1380.308
1390.864
140.891
1400.705
1410.15
1420.608
1430.00982
1440.558
1450.43
1460.183
1470.941
1480.075
1490.108
150.752
1500.815
1510.234
1520.334
1530.797
1540.869
1550.166
1560.896
1570.497
1580.426
1590.685
160.336
1600.318
1610.356
1620.302
1630.618
1640.866
1650.789
1660.23
1670.34
1680.0386
1690.207
170.761
180.215
190.143
20.435
200.313
210.817
220.135
230.0267
240.606
250.777
260.323
270.412
280.738
290.982
30.0542
300.946
310.584
320.0385
330.588
340.101
350.448
360.0334
370.0619
380.596
390.238
40.423
400.38
410.00464
420.197
430.0678
440.905
450.675
460.568
470.692
480.987
490.253
50.259
500.33
510.798
520.726
530.747
540.756
550.677
560.302
570.443
580.264
590.0772
60.893
600.0545
610.807
620.0839
630.281
640.7
650.0549
660.0247
670.187
680.442
690.685
70.383
700.319
710.107
720.35
730.23
740.269
750.504
760.353
770.0407
780.416
790.141
80.665
800.00336
810.151
820.343
830.544
840.74
850.517
860.342
870.102
880.213
890.037
90.00612
900.233
910.145
920.536
930.0607
940.737
950.695
960.0628
970.842
980.703
990.827



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: CNhs11943


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)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
5093 (thoracic cancer)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000310 (breast)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000915 (thoracic segment of trunk)
0001062 (anatomical entity)
0001443 (chest)

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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