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FF:13163-141B4: 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 17:24, 29 March 2012


Name:MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep3
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-penis-0.0113
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-lymphoma0.231
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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: CNhs12703

Jaspar motifP-value
MA0002.20.0656
MA0003.10.701
MA0004.10.0259
MA0006.10.648
MA0007.10.796
MA0009.10.595
MA0014.10.073
MA0017.10.229
MA0018.20.421
MA0019.10.0673
MA0024.19.00929e-4
MA0025.10.111
MA0027.10.864
MA0028.12.49865e-5
MA0029.10.0779
MA0030.10.0479
MA0031.10.168
MA0035.20.165
MA0038.18.42852e-5
MA0039.25.60138e-4
MA0040.10.745
MA0041.10.325
MA0042.10.751
MA0043.10.124
MA0046.10.0976
MA0047.20.0245
MA0048.10.347
MA0050.11.16822e-4
MA0051.10.0175
MA0052.10.786
MA0055.10.0176
MA0057.10.951
MA0058.10.0136
MA0059.10.618
MA0060.12.98229e-32
MA0061.10.0018
MA0062.22.24424e-7
MA0065.20.738
MA0066.10.58
MA0067.10.083
MA0068.10.66
MA0069.10.663
MA0070.10.035
MA0071.10.879
MA0072.10.415
MA0073.10.981
MA0074.10.932
MA0076.12.2941e-5
MA0077.10.543
MA0078.10.265
MA0079.20.391
MA0080.27.31334e-6
MA0081.10.775
MA0083.10.58
MA0084.10.397
MA0087.10.682
MA0088.10.631
MA0090.10.813
MA0091.10.126
MA0092.10.526
MA0093.10.0161
MA0099.20.109
MA0100.10.189
MA0101.10.19
MA0102.20.00296
MA0103.15.03091e-6
MA0104.20.103
MA0105.14.64729e-5
MA0106.10.251
MA0107.10.0523
MA0108.20.00583
MA0111.10.416
MA0112.20.812
MA0113.10.237
MA0114.10.94
MA0115.10.701
MA0116.10.00399
MA0117.10.267
MA0119.10.103
MA0122.10.147
MA0124.10.129
MA0125.16.99582e-4
MA0131.10.0669
MA0135.10.0371
MA0136.10.0946
MA0137.20.343
MA0138.20.362
MA0139.10.409
MA0140.10.354
MA0141.10.474
MA0142.10.995
MA0143.10.0655
MA0144.10.114
MA0145.10.984
MA0146.10.147
MA0147.10.171
MA0148.10.0955
MA0149.10.136
MA0150.10.0362
MA0152.10.45
MA0153.10.196
MA0154.10.0701
MA0155.10.754
MA0156.10.42
MA0157.10.545
MA0159.10.568
MA0160.10.785
MA0162.10.458
MA0163.10.00351
MA0164.10.699
MA0258.10.797
MA0259.10.0631



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: CNhs12703

Novel motifP-value
10.132
100.545
1000.668
1010.09
1020.263
1030.102
1040.933
1050.346
1060.0153
1070.0313
1080.833
1090.0507
110.441
1100.688
1110.0163
1120.2
1130.0976
1140.0445
1150.146
1160.338
1170.423
1180.605
1190.38
120.482
1200.569
1210.891
1220.169
1230.0115
1240.34
1250.345
1260.815
1270.69
1280.0159
1290.945
130.494
1300.00576
1310.221
1320.511
1330.00803
1340.0719
1350.356
1360.00139
1370.0976
1380.15
1390.133
140.875
1400.0583
1410.834
1420.253
1430.0932
1440.413
1450.163
1460.57
1470.906
1480.0013
1490.158
150.369
1500.79
1510.0488
1520.524
1530.105
1540.195
1550.0804
1560.899
1570.271
1580.292
1590.885
160.482
1600.805
1610.611
1620.943
1630.707
1640.426
1650.178
1660.0752
1670.605
1680.25
1690.701
170.655
180.0802
190.312
20.553
200.392
210.217
220.598
230.00221
240.976
250.802
260.438
270.689
280.911
290.714
30.0659
300.412
310.524
320.091
330.3
340.274
350.0343
360.394
370.17
380.933
390.333
40.379
400.257
410.22
420.301
430.0841
440.283
450.766
460.169
470.667
480.974
490.128
50.178
500.515
510.76
520.318
530.112
540.582
550.409
560.701
570.306
580.405
590.539
60.716
600.0461
610.548
620.142
630.204
640.807
650.158
660.00301
670.495
680.737
690.327
70.939
700.0908
710.414
720.519
730.98
740.0223
750.823
760.69
770.215
780.96
790.262
80.471
800.0681
810.111
820.287
830.167
840.654
850.0712
860.572
870.00198
880.975
890.0863
90.181
901.81959e-5
910.0698
920.0433
930.578
940.122
950.0157
960.171
970.898
980.411
990.956



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: CNhs12703


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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