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FF:12642-134G5: 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 17:31, 29 March 2012


Name:Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueaorta
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell, vascular associated
cell lineNA
companyNA
collaborationLevon Khachigian (University of New South Wales)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.00938
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-0.229
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13339

Jaspar motifP-value
MA0002.20.374
MA0003.10.418
MA0004.10.396
MA0006.10.247
MA0007.10.451
MA0009.10.73
MA0014.10.998
MA0017.10.146
MA0018.27.48482e-6
MA0019.10.927
MA0024.15.57872e-5
MA0025.13.75921e-4
MA0027.10.877
MA0028.10.416
MA0029.10.715
MA0030.10.0781
MA0031.10.234
MA0035.20.0666
MA0038.19.85926e-4
MA0039.20.0896
MA0040.10.62
MA0041.10.36
MA0042.10.817
MA0043.12.87274e-6
MA0046.10.0967
MA0047.20.249
MA0048.10.308
MA0050.10.279
MA0051.10.871
MA0052.10.0756
MA0055.10.738
MA0057.10.625
MA0058.10.228
MA0059.10.295
MA0060.13.75844e-12
MA0061.10.0793
MA0062.20.0139
MA0065.20.0429
MA0066.10.0402
MA0067.10.0159
MA0068.10.628
MA0069.10.295
MA0070.10.202
MA0071.10.61
MA0072.10.576
MA0073.10.64
MA0074.10.113
MA0076.10.0963
MA0077.10.409
MA0078.10.48
MA0079.20.0846
MA0080.20.0132
MA0081.10.31
MA0083.10.00572
MA0084.10.143
MA0087.10.411
MA0088.10.351
MA0090.10.272
MA0091.10.0934
MA0092.10.124
MA0093.10.325
MA0099.20.162
MA0100.10.261
MA0101.10.571
MA0102.20.201
MA0103.10.673
MA0104.20.522
MA0105.11.01347e-4
MA0106.10.00295
MA0107.10.564
MA0108.20.549
MA0111.10.84
MA0112.20.00101
MA0113.10.541
MA0114.10.319
MA0115.10.607
MA0116.10.0152
MA0117.10.845
MA0119.10.0323
MA0122.10.413
MA0124.10.737
MA0125.10.503
MA0131.10.237
MA0135.10.155
MA0136.10.0107
MA0137.20.303
MA0138.20.285
MA0139.10.237
MA0140.10.32
MA0141.10.143
MA0142.10.359
MA0143.10.34
MA0144.10.39
MA0145.10.333
MA0146.10.874
MA0147.10.897
MA0148.10.718
MA0149.10.0938
MA0150.10.877
MA0152.10.092
MA0153.10.195
MA0154.10.0281
MA0155.10.238
MA0156.10.0505
MA0157.10.953
MA0159.10.0974
MA0160.10.935
MA0162.10.0424
MA0163.16.28794e-7
MA0164.10.793
MA0258.10.029
MA0259.10.258



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: CNhs13339

Novel motifP-value
10.103
100.203
1000.447
1010.832
1020.93
1030.12
1040.978
1050.344
1060.0348
1070.086
1080.189
1090.183
110.0398
1100.0607
1110.0821
1120.0908
1130.245
1140.013
1150.082
1160.107
1170.185
1180.295
1190.0641
120.968
1200.0229
1210.419
1220.0594
1230.657
1240.95
1250.265
1260.368
1270.68
1280.0519
1290.533
130.287
1300.193
1310.972
1320.763
1330.734
1340.966
1350.0999
1360.853
1370.603
1380.859
1390.522
140.77
1400.16
1410.731
1420.757
1430.039
1440.329
1450.158
1460.587
1470.232
1480.00476
1490.0358
150.345
1500.212
1510.632
1520.133
1530.836
1540.928
1550.141
1560.549
1570.276
1580.0579
1590.186
160.0425
1600.105
1610.777
1620.173
1630.815
1640.0364
1650.317
1660.395
1670.208
1680.439
1690.0375
170.0771
180.0526
190.0845
20.533
200.887
210.269
220.425
230.209
240.637
250.526
260.0931
270.226
280.599
290.0788
30.0772
300.786
310.472
322.55176e-5
330.414
340.803
350.0856
360.129
370.0272
380.667
390.198
40.914
400.515
410.854
420.721
430.121
440.018
450.835
460.0296
470.241
480.248
490.41
50.441
500.672
510.577
520.532
530.558
540.564
550.353
560.721
570.304
580.901
590.0702
60.504
600.238
610.794
620.285
630.141
640.519
650.246
660.32
670.371
680.629
690.393
70.959
700.0177
710.0543
720.737
730.0399
740.049
750.196
760.594
770.0269
780.643
795.26115e-4
80.0192
800.617
810.254
820.0968
830.597
840.998
850.0416
860.438
870.12
880.178
890.0289
90.467
900.0408
910.244
920.161
930.682
940.174
950.268
960.535
970.506
980.858
990.08



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: CNhs13339


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
0000003 (native cell)

DOID: Disease
0000465 (material anatomical entity)

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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