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FF:13097-140D1: Difference between revisions

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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 17:19, 29 March 2012


Name:MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep2
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
ageNA
cell typemammary gland epithelial cell
cell lineMCF7
companyNA
collaborationMariko Okada Hatakeyama (RIKEN RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)Repurified by minelute
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-penis0.0445
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs12475

Jaspar motifP-value
MA0002.20.0474
MA0003.10.69
MA0004.10.0698
MA0006.10.669
MA0007.10.754
MA0009.10.835
MA0014.10.145
MA0017.10.0624
MA0018.20.636
MA0019.10.208
MA0024.10.00181
MA0025.10.17
MA0027.10.881
MA0028.17.93636e-4
MA0029.10.143
MA0030.10.142
MA0031.10.518
MA0035.20.353
MA0038.10.00119
MA0039.20.00115
MA0040.10.978
MA0041.10.502
MA0042.10.948
MA0043.10.176
MA0046.10.0892
MA0047.20.0466
MA0048.10.432
MA0050.13.35482e-5
MA0051.10.0115
MA0052.10.498
MA0055.10.0196
MA0057.10.689
MA0058.10.0328
MA0059.10.772
MA0060.13.422e-27
MA0061.10.00108
MA0062.26.46199e-6
MA0065.20.407
MA0066.10.803
MA0067.10.173
MA0068.10.86
MA0069.10.477
MA0070.10.0274
MA0071.10.826
MA0072.10.591
MA0073.10.84
MA0074.10.705
MA0076.11.50936e-4
MA0077.10.576
MA0078.10.33
MA0079.20.281
MA0080.29.2531e-8
MA0081.10.475
MA0083.10.331
MA0084.10.432
MA0087.10.758
MA0088.10.731
MA0090.10.895
MA0091.10.091
MA0092.10.599
MA0093.10.0646
MA0099.20.0249
MA0100.10.369
MA0101.10.0621
MA0102.20.00566
MA0103.12.24802e-6
MA0104.20.423
MA0105.15.75809e-6
MA0106.10.412
MA0107.10.00516
MA0108.20.00523
MA0111.10.387
MA0112.20.555
MA0113.10.493
MA0114.10.507
MA0115.10.917
MA0116.10.00112
MA0117.10.253
MA0119.10.0646
MA0122.10.176
MA0124.10.223
MA0125.10.0123
MA0131.10.126
MA0135.10.0949
MA0136.10.00776
MA0137.20.0997
MA0138.20.801
MA0139.10.666
MA0140.10.404
MA0141.10.533
MA0142.10.82
MA0143.10.0917
MA0144.10.037
MA0145.10.796
MA0146.10.0601
MA0147.10.609
MA0148.10.181
MA0149.10.363
MA0150.10.017
MA0152.10.529
MA0153.10.36
MA0154.10.0462
MA0155.10.522
MA0156.10.0775
MA0157.10.991
MA0159.10.459
MA0160.10.843
MA0162.10.689
MA0163.10.00396
MA0164.10.843
MA0258.10.814
MA0259.10.112



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: CNhs12475

Novel motifP-value
10.172
100.619
1000.571
1010.139
1020.334
1030.165
1040.872
1050.154
1060.0264
1070.0823
1080.665
1090.092
110.505
1100.976
1110.0279
1120.24
1130.0848
1140.0131
1150.246
1160.547
1170.387
1180.319
1190.313
120.788
1200.864
1210.805
1220.453
1230.101
1240.12
1250.291
1260.779
1270.802
1280.0696
1290.505
130.572
1300.00194
1310.21
1320.814
1330.0092
1340.154
1350.299
1360.00155
1370.0975
1380.133
1390.0596
141
1400.299
1410.789
1420.267
1430.0359
1440.345
1450.273
1460.488
1470.746
1484.61885e-4
1490.215
150.404
1500.978
1510.157
1520.778
1530.0883
1540.394
1550.0492
1560.768
1570.423
1580.268
1590.655
160.491
1600.441
1610.639
1620.893
1630.667
1640.449
1650.37
1660.157
1670.891
1680.235
1690.967
170.829
180.0868
190.236
20.44
200.28
210.248
220.637
230.00184
240.946
250.937
260.317
270.571
280.845
290.842
30.112
300.436
310.471
320.152
330.523
340.242
350.103
360.281
370.16
380.994
390.516
40.621
400.243
410.174
420.194
430.104
440.266
450.903
460.139
470.883
480.977
490.146
50.126
500.479
510.539
520.313
530.132
540.377
550.439
560.41
570.347
580.297
590.317
60.531
600.0373
610.721
620.068
630.239
640.784
650.268
660.0307
670.514
680.961
690.639
70.655
700.0424
710.361
720.578
730.791
740.0659
750.99
760.979
770.411
780.944
790.263
80.415
800.0469
810.134
820.286
830.367
840.818
850.0701
860.464
870.00296
880.667
890.0853
90.151
907.07333e-5
910.0964
920.0211
930.188
940.121
950.02
960.0849
970.964
980.28
990.937



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: CNhs12475


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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