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FF:11890-125D9: 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 treated with Streptococci strain 5448, 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 number1a
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-penis0.0142
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0.849
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.463
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: CNhs13477

Jaspar motifP-value
MA0002.20.0669
MA0003.10.848
MA0004.10.153
MA0006.10.518
MA0007.10.391
MA0009.10.597
MA0014.10.587
MA0017.10.446
MA0018.20.839
MA0019.10.907
MA0024.11.85755e-7
MA0025.10.0671
MA0027.10.922
MA0028.11.83269e-6
MA0029.10.483
MA0030.10.686
MA0031.10.1
MA0035.20.698
MA0038.10.889
MA0039.20.0468
MA0040.10.281
MA0041.10.413
MA0042.10.527
MA0043.10.164
MA0046.10.778
MA0047.20.911
MA0048.10.0248
MA0050.10.131
MA0051.10.712
MA0052.10.00199
MA0055.11.48636e-4
MA0057.10.277
MA0058.10.0754
MA0059.10.00689
MA0060.10.225
MA0061.10.119
MA0062.20.00389
MA0065.20.0111
MA0066.10.757
MA0067.10.293
MA0068.10.00272
MA0069.10.275
MA0070.10.583
MA0071.10.0383
MA0072.10.587
MA0073.10.178
MA0074.10.489
MA0076.13.68082e-5
MA0077.10.979
MA0078.10.137
MA0079.20.323
MA0080.28.5286e-8
MA0081.10.431
MA0083.10.0146
MA0084.10.538
MA0087.10.422
MA0088.10.0374
MA0090.10.00683
MA0091.10.509
MA0092.10.796
MA0093.10.105
MA0099.20.0136
MA0100.10.608
MA0101.10.204
MA0102.20.498
MA0103.10.0217
MA0104.27.7794e-4
MA0105.10.804
MA0106.10.58
MA0107.10.0558
MA0108.20.331
MA0111.10.864
MA0112.20.0228
MA0113.10.71
MA0114.10.0143
MA0115.10.0249
MA0116.10.32
MA0117.10.973
MA0119.10.616
MA0122.10.937
MA0124.10.7
MA0125.10.483
MA0131.10.207
MA0135.10.49
MA0136.16.11778e-4
MA0137.20.0224
MA0138.20.067
MA0139.10.604
MA0140.10.401
MA0141.10.005
MA0142.10.917
MA0143.10.102
MA0144.10.359
MA0145.10.748
MA0146.10.113
MA0147.12.88815e-4
MA0148.10.246
MA0149.10.0745
MA0150.10.386
MA0152.10.464
MA0153.10.0681
MA0154.10.773
MA0155.10.296
MA0156.10.0859
MA0157.10.0908
MA0159.10.0749
MA0160.10.0297
MA0162.10.126
MA0163.10.0227
MA0164.10.334
MA0258.10.62
MA0259.10.027



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: CNhs13477

Novel motifP-value
10.0941
100.0621
1000.0249
1010.231
1020.919
1030.656
1040.938
1050.161
1060.0495
1070.267
1080.822
1098.08662e-4
110.801
1100.21
1110.82
1120.451
1130.00142
1140.9
1150.529
1160.249
1170.114
1180.0904
1190.61
120.747
1200.0521
1210.492
1220.21
1230.24
1240.539
1250.915
1260.834
1270.24
1280.00103
1290.281
136.82471e-5
1300.673
1310.442
1320.398
1330.305
1340.988
1350.0841
1360.00316
1370.281
1380.843
1390.0781
140.395
1400.345
1410.506
1420.695
1430.166
1440.41
1450.349
1460.515
1470.907
1480.433
1490.71
150.887
1500.463
1510.733
1520.798
1530.567
1540.435
1550.432
1560.0411
1570.12
1580.142
1590.199
160.784
1600.387
1610.507
1620.765
1630.273
1640.00858
1650.941
1660.0329
1670.176
1680.347
1690.144
170.991
180.156
190.974
20.557
200.0758
210.256
220.931
230.00385
240.687
250.365
260.632
270.927
280.858
290.0168
30.805
300.368
310.579
320.182
330.166
340.232
350.768
360.162
370.197
380.931
390.925
40.196
400.0172
410.0958
420.914
430.508
440.0383
450.179
460.785
470.352
480.44
490.208
50.187
500.855
510.641
520.368
530.138
540.51
550.0287
560.95
570.623
580.784
590.781
60.539
600.428
610.0413
620.829
630.492
640.669
650.449
660.748
670.636
680.678
690.843
70.0484
700.489
710.0235
720.803
730.214
740.11
750.096
760.177
770.521
780.169
790.894
80.0954
800.0333
810.31
820.196
830.544
840.559
850.0301
860.868
870.00473
880.751
890.753
90.528
900.0589
910.0196
920.0827
930.349
940.421
950.00104
960.46
970.742
980.991
990.359



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: CNhs13477


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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