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FF:11896-125E6: 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_rep3
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 number2c
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-0.0366
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0.805
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.486
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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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: CNhs13499

Jaspar motifP-value
MA0002.20.244
MA0003.10.779
MA0004.10.109
MA0006.10.478
MA0007.10.687
MA0009.10.512
MA0014.10.566
MA0017.10.13
MA0018.20.714
MA0019.10.892
MA0024.16.35105e-8
MA0025.10.418
MA0027.10.516
MA0028.13.19456e-5
MA0029.10.775
MA0030.10.344
MA0031.10.123
MA0035.20.291
MA0038.10.789
MA0039.20.0577
MA0040.10.703
MA0041.10.366
MA0042.10.485
MA0043.10.19
MA0046.10.902
MA0047.20.716
MA0048.10.129
MA0050.10.0052
MA0051.10.766
MA0052.10.0249
MA0055.11.59644e-4
MA0057.10.173
MA0058.10.0388
MA0059.10.00513
MA0060.10.239
MA0061.10.5
MA0062.20.0137
MA0065.20.0034
MA0066.10.424
MA0067.10.476
MA0068.17.34898e-7
MA0069.10.237
MA0070.10.639
MA0071.10.0161
MA0072.10.508
MA0073.10.526
MA0074.10.446
MA0076.11.95894e-4
MA0077.10.659
MA0078.10.286
MA0079.20.249
MA0080.25.82923e-7
MA0081.10.45
MA0083.10.0193
MA0084.10.187
MA0087.10.237
MA0088.10.0363
MA0090.10.0269
MA0091.10.536
MA0092.10.549
MA0093.10.0699
MA0099.20.92
MA0100.10.385
MA0101.10.459
MA0102.20.459
MA0103.10.0129
MA0104.25.88423e-4
MA0105.10.467
MA0106.10.428
MA0107.10.188
MA0108.20.0641
MA0111.10.611
MA0112.20.00165
MA0113.10.796
MA0114.10.0031
MA0115.10.0136
MA0116.10.122
MA0117.10.631
MA0119.10.388
MA0122.10.924
MA0124.10.955
MA0125.10.695
MA0131.10.42
MA0135.10.543
MA0136.10.0125
MA0137.20.00796
MA0138.20.207
MA0139.10.451
MA0140.10.847
MA0141.13.13853e-4
MA0142.10.942
MA0143.10.131
MA0144.10.348
MA0145.10.791
MA0146.10.198
MA0147.11.71582e-4
MA0148.10.124
MA0149.10.0141
MA0150.10.797
MA0152.10.432
MA0153.10.104
MA0154.10.788
MA0155.10.373
MA0156.10.163
MA0157.10.134
MA0159.10.0299
MA0160.10.00129
MA0162.10.124
MA0163.10.00328
MA0164.10.277
MA0258.10.229
MA0259.10.0286



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: CNhs13499

Novel motifP-value
10.0294
100.0469
1000.0409
1010.276
1020.911
1030.493
1040.851
1050.174
1060.0967
1070.184
1080.783
1090.00111
110.468
1100.228
1110.272
1120.779
1130.00478
1140.187
1150.524
1160.218
1170.11
1180.0822
1190.255
120.477
1200.0145
1210.352
1220.152
1230.063
1240.771
1250.505
1260.564
1270.101
1280.00115
1290.693
132.64397e-4
1300.765
1310.175
1320.95
1330.119
1340.878
1350.316
1360.00925
1370.292
1380.605
1390.263
140.34
1400.596
1410.0561
1420.868
1430.615
1440.571
1450.24
1460.996
1470.579
1480.392
1490.678
150.255
1500.466
1510.863
1520.662
1530.517
1540.285
1550.183
1560.0145
1570.116
1580.356
1590.277
160.503
1600.337
1610.228
1620.886
1630.32
1640.0205
1650.9
1660.0181
1670.111
1680.704
1690.143
170.789
180.54
190.794
20.612
200.0942
210.13
220.928
230.0142
240.233
250.219
260.41
270.87
280.912
290.0066
30.879
300.394
310.696
320.187
330.141
340.267
350.789
360.0479
370.223
380.571
390.833
40.239
400.00591
410.346
420.765
430.896
440.0348
450.301
460.908
470.158
480.388
490.499
50.584
500.932
510.869
520.342
530.217
540.607
550.0609
560.788
570.286
580.703
590.82
60.877
600.879
610.0294
620.59
630.42
640.692
650.761
660.843
670.734
680.597
690.885
70.0194
700.851
710.00993
720.841
730.352
740.249
750.0986
760.175
770.294
780.1
790.937
80.0313
800.0559
810.522
820.301
830.439
840.352
850.0874
860.921
870.0068
880.989
890.513
90.72
900.0278
910.0082
920.37
930.207
940.805
950.011
960.593
970.888
980.712
990.705



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: CNhs13499


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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