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FF:11898-125E8: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 17:33, 29 March 2012


Name:Hep-2 cells mock treated, biol_rep1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age56
cell typeunclassifiable
cell lineHep-2
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3a
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-penis-0.0122
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0.837
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.501
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs13479

Jaspar motifP-value
MA0002.20.0534
MA0003.10.866
MA0004.10.123
MA0006.10.562
MA0007.10.304
MA0009.10.592
MA0014.10.704
MA0017.10.642
MA0018.20.899
MA0019.10.968
MA0024.16.96187e-8
MA0025.10.127
MA0027.10.805
MA0028.11.39693e-6
MA0029.10.54
MA0030.10.494
MA0031.10.187
MA0035.20.599
MA0038.10.882
MA0039.20.057
MA0040.10.403
MA0041.10.358
MA0042.10.43
MA0043.10.111
MA0046.10.437
MA0047.20.888
MA0048.10.0277
MA0050.10.0771
MA0051.10.697
MA0052.10.00572
MA0055.14.66797e-5
MA0057.10.233
MA0058.10.0457
MA0059.10.00835
MA0060.10.0277
MA0061.10.0703
MA0062.20.004
MA0065.20.0159
MA0066.10.722
MA0067.10.231
MA0068.10.00319
MA0069.10.317
MA0070.10.582
MA0071.10.0585
MA0072.10.608
MA0073.10.169
MA0074.10.565
MA0076.14.2829e-5
MA0077.10.949
MA0078.10.19
MA0079.20.56
MA0080.23.31714e-8
MA0081.10.267
MA0083.10.00426
MA0084.10.402
MA0087.10.552
MA0088.10.0159
MA0090.10.00305
MA0091.10.537
MA0092.10.839
MA0093.10.0771
MA0099.20.00467
MA0100.10.371
MA0101.10.163
MA0102.20.718
MA0103.10.0452
MA0104.20.00106
MA0105.10.656
MA0106.10.562
MA0107.10.044
MA0108.20.24
MA0111.10.881
MA0112.20.0388
MA0113.10.865
MA0114.10.0227
MA0115.10.0467
MA0116.10.404
MA0117.10.787
MA0119.10.751
MA0122.10.94
MA0124.10.841
MA0125.10.398
MA0131.10.298
MA0135.10.898
MA0136.18.2326e-4
MA0137.20.0288
MA0138.20.106
MA0139.10.558
MA0140.10.566
MA0141.10.00458
MA0142.10.863
MA0143.10.0861
MA0144.10.357
MA0145.10.847
MA0146.10.175
MA0147.14.69236e-4
MA0148.10.371
MA0149.10.086
MA0150.10.35
MA0152.10.527
MA0153.10.0285
MA0154.10.531
MA0155.10.242
MA0156.10.138
MA0157.10.17
MA0159.10.166
MA0160.10.0261
MA0162.10.156
MA0163.10.0549
MA0164.10.331
MA0258.10.747
MA0259.10.0226



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: CNhs13479

Novel motifP-value
10.127
100.093
1000.0237
1010.194
1020.904
1030.835
1040.887
1050.183
1060.0131
1070.151
1080.729
1090.00141
110.995
1100.291
1110.713
1120.349
1130.00143
1140.873
1150.756
1160.244
1170.145
1180.203
1190.749
120.925
1200.0518
1210.506
1220.176
1230.206
1240.687
1250.901
1260.837
1270.274
1281.72143e-4
1290.357
131.03398e-4
1300.434
1310.4
1320.5
1330.181
1340.949
1350.0457
1360.00347
1370.223
1380.711
1390.0355
140.374
1400.206
1410.526
1420.612
1430.219
1440.381
1450.231
1460.671
1470.793
1480.574
1490.555
150.95
1500.637
1510.552
1520.683
1530.562
1540.404
1550.652
1560.0311
1570.117
1580.114
1590.218
160.937
1600.418
1610.629
1620.851
1630.294
1640.0154
1650.989
1660.0899
1670.237
1680.255
1690.29
170.847
180.249
190.853
20.497
200.105
210.418
220.886
230.00168
240.764
250.366
260.994
270.686
280.758
290.0268
30.61
300.44
310.521
320.133
330.157
340.194
350.776
360.172
370.329
380.942
390.97
40.201
400.018
410.107
420.954
430.418
440.0655
450.206
460.558
470.384
480.455
490.236
50.217
500.856
510.63
520.27
530.0855
540.484
550.0469
560.902
570.528
580.89
590.875
60.704
600.371
610.0454
620.903
630.548
640.778
650.407
660.529
670.773
680.511
690.96
70.0366
700.296
710.0533
720.817
730.318
740.0615
750.104
760.21
770.558
780.186
790.991
80.13
800.029
810.233
820.115
830.64
840.502
850.0189
860.9
870.00623
880.817
890.644
90.559
900.0363
910.0104
920.0728
930.29
940.419
950.00191
960.411
970.879
980.848
990.374



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: CNhs13479


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
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)

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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