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FF:10080-102A8: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:53, 29 March 2012


Name:breast, adult, donor1
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 stage77 years old adult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number808002
catalog numberCat:AM6952
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-penis0.0308
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-lymphoma-0.35
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11792

Jaspar motifP-value
MA0002.20.0339
MA0003.10.508
MA0004.10.742
MA0006.10.39
MA0007.10.78
MA0009.10.03
MA0014.10.871
MA0017.10.725
MA0018.20.329
MA0019.10.0252
MA0024.10.023
MA0025.10.921
MA0027.10.606
MA0028.11.49288e-5
MA0029.10.99
MA0030.17.15115e-4
MA0031.10.00439
MA0035.20.693
MA0038.10.801
MA0039.20.368
MA0040.10.623
MA0041.10.152
MA0042.10.22
MA0043.10.971
MA0046.10.344
MA0047.20.0149
MA0048.10.138
MA0050.10.751
MA0051.10.713
MA0052.10.00128
MA0055.10.0142
MA0057.10.813
MA0058.10.594
MA0059.10.0412
MA0060.10.459
MA0061.10.00725
MA0062.24.77824e-8
MA0065.20.453
MA0066.10.172
MA0067.10.505
MA0068.15.12863e-5
MA0069.10.543
MA0070.10.744
MA0071.10.501
MA0072.10.487
MA0073.10.979
MA0074.10.502
MA0076.16.88335e-8
MA0077.10.337
MA0078.10.32
MA0079.20.218
MA0080.20.819
MA0081.10.37
MA0083.10.00639
MA0084.10.976
MA0087.10.445
MA0088.10.014
MA0090.10.0605
MA0091.10.689
MA0092.10.797
MA0093.10.747
MA0099.21.67331e-6
MA0100.10.109
MA0101.10.167
MA0102.20.0192
MA0103.10.227
MA0104.20.0235
MA0105.18.87908e-7
MA0106.10.0977
MA0107.10.345
MA0108.28.30402e-18
MA0111.10.546
MA0112.20.0678
MA0113.10.491
MA0114.10.912
MA0115.10.877
MA0116.11.95757e-4
MA0117.10.238
MA0119.10.484
MA0122.10.435
MA0124.10.88
MA0125.10.904
MA0131.10.195
MA0135.10.0528
MA0136.10.0394
MA0137.23.45748e-6
MA0138.20.745
MA0139.10.0272
MA0140.10.392
MA0141.10.0951
MA0142.10.847
MA0143.10.447
MA0144.10.0109
MA0145.10.455
MA0146.10.441
MA0147.10.01
MA0148.10.0369
MA0149.10.148
MA0150.10.0217
MA0152.10.216
MA0153.10.0866
MA0154.10.0994
MA0155.10.642
MA0156.10.0124
MA0157.10.0963
MA0159.10.258
MA0160.10.447
MA0162.10.796
MA0163.13.28526e-10
MA0164.10.528
MA0258.10.0461
MA0259.10.114



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: CNhs11792

Novel motifP-value
10.012
100.0449
1000.244
1010.373
1020.456
1030.154
1040.615
1050.745
1060.694
1070.319
1080.941
1090.0715
110.1
1100.0971
1110.0313
1120.751
1130.35
1140.00368
1150.0676
1160.593
1170.0069
1180.076
1190.829
120.673
1200.189
1210.741
1220.832
1230.0081
1240.24
1250.251
1260.475
1270.924
1280.868
1290.378
130.0625
1300.812
1310.593
1320.0743
1330.643
1340.882
1350.192
1360.742
1370.715
1380.232
1390.563
140.649
1400.0571
1410.447
1420.304
1430.00247
1440.815
1450.663
1460.984
1470.333
1480.275
1490.46
150.0587
1500.565
1510.789
1520.167
1530.733
1540.24
1550.99
1560.737
1570.342
1580.253
1590.734
160.11
1600.863
1610.354
1620.49
1630.779
1640.0584
1650.66
1660.967
1670.027
1680.734
1690.605
170.506
180.0878
190.774
20.29
200.197
210.445
220.699
230.202
240.391
250.321
260.116
270.659
280.526
290.0128
30.0708
300.0314
310.917
320.307
330.3
340.27
350.0448
360.041
370.173
380.824
390.29
40.343
400.157
410.452
420.112
430.262
440.549
450.237
460.0799
470.0286
480.114
490.0765
50.807
500.741
510.513
520.194
530.665
540.992
550.633
560.707
570.103
580.514
590.759
60.978
600.595
610.214
620.362
630.601
640.258
650.913
660.0953
670.691
680.334
690.438
70.405
700.00571
710.0182
720.938
730.583
740.781
750.0259
760.0358
770.247
780.31
790.884
80.418
800.326
810.337
820.301
830.496
840.67
850.467
860.758
870.374
880.693
890.222
90.306
900.0334
910.488
920.625
930.0165
940.077
950.0865
960.42
970.622
980.048
990.414



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: CNhs11792


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

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000310 (breast)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001443 (chest)
0001891 (midbrain)
0002050 (embryonic structure)
0002298 (brainstem)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002950 (regional part of midbrain)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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