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FF:11895-125E5: 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 17:35, 29 March 2012


Name:Hep-2 cells treated with Streptococci strain JRS4, 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
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 number2b
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-0.014
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0.785
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.471
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
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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: CNhs13498

Jaspar motifP-value
MA0002.20.199
MA0003.10.762
MA0004.10.0585
MA0006.10.547
MA0007.10.527
MA0009.10.554
MA0014.10.383
MA0017.10.135
MA0018.20.772
MA0019.10.797
MA0024.16.50421e-8
MA0025.10.027
MA0027.10.844
MA0028.11.87786e-5
MA0029.10.454
MA0030.10.276
MA0031.10.287
MA0035.20.696
MA0038.10.847
MA0039.20.0608
MA0040.10.484
MA0041.10.33
MA0042.10.394
MA0043.10.134
MA0046.10.765
MA0047.20.735
MA0048.10.117
MA0050.10.0726
MA0051.10.794
MA0052.10.0588
MA0055.19.89264e-5
MA0057.10.238
MA0058.10.0103
MA0059.10.00427
MA0060.10.153
MA0061.10.447
MA0062.20.00785
MA0065.20.00567
MA0066.10.475
MA0067.10.496
MA0068.13.20424e-4
MA0069.10.28
MA0070.10.644
MA0071.10.00788
MA0072.10.561
MA0073.10.225
MA0074.10.394
MA0076.15.36283e-5
MA0077.10.9
MA0078.10.322
MA0079.20.339
MA0080.21.27419e-7
MA0081.10.323
MA0083.10.0072
MA0084.10.282
MA0087.10.459
MA0088.10.0337
MA0090.10.00499
MA0091.10.545
MA0092.10.704
MA0093.10.0295
MA0099.20.633
MA0100.10.267
MA0101.10.404
MA0102.20.523
MA0103.10.00887
MA0104.27.68932e-4
MA0105.10.394
MA0106.10.504
MA0107.10.161
MA0108.20.0512
MA0111.10.608
MA0112.20.00493
MA0113.10.779
MA0114.10.0056
MA0115.10.0477
MA0116.10.167
MA0117.10.83
MA0119.10.625
MA0122.10.86
MA0124.10.984
MA0125.10.524
MA0131.10.54
MA0135.10.832
MA0136.10.0018
MA0137.20.0394
MA0138.20.0851
MA0139.10.63
MA0140.10.711
MA0141.17.53259e-4
MA0142.10.862
MA0143.10.171
MA0144.10.433
MA0145.10.63
MA0146.10.182
MA0147.13.52608e-4
MA0148.10.137
MA0149.10.0269
MA0150.10.633
MA0152.10.678
MA0153.10.0212
MA0154.10.779
MA0155.10.445
MA0156.10.14
MA0157.10.262
MA0159.10.071
MA0160.10.00166
MA0162.10.109
MA0163.10.00474
MA0164.10.272
MA0258.10.3
MA0259.10.0404



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: CNhs13498

Novel motifP-value
10.0301
100.0523
1000.0159
1010.203
1020.968
1030.839
1040.743
1050.258
1060.0473
1070.18
1080.645
1099.27522e-4
110.57
1100.213
1110.359
1120.281
1130.00525
1140.465
1150.999
1160.186
1170.149
1180.0502
1190.305
120.702
1200.0849
1210.499
1220.108
1230.315
1240.833
1250.646
1260.749
1270.123
1287.53661e-4
1290.468
131.14885e-4
1300.554
1310.408
1320.877
1330.0979
1340.805
1350.159
1360.0115
1370.167
1380.462
1390.0911
140.555
1400.461
1410.21
1420.674
1430.249
1440.455
1450.336
1460.863
1470.474
1480.415
1490.455
150.358
1500.726
1510.76
1520.671
1530.796
1540.332
1550.617
1560.105
1570.0842
1580.184
1590.139
160.53
1600.243
1610.383
1620.356
1630.196
1640.00924
1650.298
1660.0362
1670.196
1680.182
1690.132
170.862
180.259
190.98
20.555
200.15
210.194
220.902
230.0216
240.427
250.124
260.645
270.867
280.871
290.012
30.801
300.447
310.678
320.167
330.111
340.237
350.876
360.0534
370.261
380.518
390.991
40.149
400.00541
410.166
420.785
430.77
440.0462
450.277
460.748
470.142
480.244
490.385
50.497
500.842
510.722
520.306
530.171
540.6
550.0531
560.902
570.408
580.912
590.995
60.491
600.528
610.0685
620.559
630.34
640.574
650.611
660.614
670.898
680.596
690.875
70.0168
700.874
710.0137
720.991
730.332
740.175
750.115
760.124
770.337
780.0986
790.649
80.0578
800.0802
810.281
820.247
830.84
840.484
850.0574
860.961
870.0044
880.902
890.645
90.606
900.0618
910.0245
920.116
930.204
940.763
950.0234
960.442
970.928
980.465
990.309



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: CNhs13498


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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