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FF:11891-125E1: 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 5448, 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 number1b
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-0.0359
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0.779
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.469
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: CNhs13496

Jaspar motifP-value
MA0002.20.11
MA0003.10.908
MA0004.10.0913
MA0006.10.455
MA0007.10.266
MA0009.10.631
MA0014.10.734
MA0017.10.417
MA0018.20.884
MA0019.10.66
MA0024.16.01466e-9
MA0025.10.209
MA0027.10.908
MA0028.13.86065e-6
MA0029.10.79
MA0030.10.326
MA0031.10.216
MA0035.20.326
MA0038.10.881
MA0039.20.00919
MA0040.10.559
MA0041.10.261
MA0042.10.332
MA0043.10.276
MA0046.10.256
MA0047.20.708
MA0048.10.0744
MA0050.10.0259
MA0051.10.889
MA0052.10.0066
MA0055.11.04409e-4
MA0057.10.197
MA0058.10.0493
MA0059.10.00923
MA0060.10.0378
MA0061.10.0329
MA0062.20.00583
MA0065.20.0246
MA0066.10.634
MA0067.10.317
MA0068.18.72918e-4
MA0069.10.48
MA0070.10.471
MA0071.10.0412
MA0072.10.429
MA0073.10.265
MA0074.10.669
MA0076.15.90352e-5
MA0077.10.611
MA0078.10.524
MA0079.20.433
MA0080.29.47497e-8
MA0081.10.37
MA0083.10.0278
MA0084.10.168
MA0087.10.662
MA0088.10.0503
MA0090.10.00478
MA0091.10.694
MA0092.10.705
MA0093.10.0538
MA0099.20.162
MA0100.10.26
MA0101.10.235
MA0102.20.412
MA0103.10.0189
MA0104.24.93283e-4
MA0105.10.331
MA0106.10.716
MA0107.10.0787
MA0108.20.471
MA0111.10.81
MA0112.20.0686
MA0113.10.754
MA0114.10.0286
MA0115.10.0456
MA0116.10.738
MA0117.10.923
MA0119.10.917
MA0122.10.928
MA0124.10.883
MA0125.10.218
MA0131.10.418
MA0135.10.771
MA0136.10.00203
MA0137.20.0404
MA0138.20.0571
MA0139.10.842
MA0140.10.875
MA0141.10.00265
MA0142.10.612
MA0143.10.141
MA0144.10.445
MA0145.10.709
MA0146.10.258
MA0147.12.36108e-4
MA0148.10.217
MA0149.10.0311
MA0150.10.633
MA0152.10.358
MA0153.10.00684
MA0154.10.449
MA0155.10.232
MA0156.10.153
MA0157.10.21
MA0159.10.0983
MA0160.10.0149
MA0162.10.217
MA0163.10.397
MA0164.10.389
MA0258.10.807
MA0259.10.0143



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: CNhs13496

Novel motifP-value
10.117
100.117
1000.035
1010.176
1020.686
1030.784
1040.838
1050.245
1060.013
1070.182
1080.537
1096.7025e-4
110.84
1100.333
1110.517
1120.232
1130.00269
1140.774
1150.837
1160.421
1170.263
1180.227
1190.995
120.546
1200.0601
1210.318
1220.132
1230.161
1240.842
1250.736
1260.799
1270.112
1281.14153e-4
1290.472
137.60177e-5
1300.319
1310.473
1320.379
1330.134
1340.851
1350.192
1360.00261
1370.225
1380.79
1390.0428
140.439
1400.184
1410.537
1420.673
1430.261
1440.356
1450.149
1460.962
1470.624
1480.55
1490.542
150.507
1500.717
1510.736
1520.771
1530.525
1540.339
1550.632
1560.0379
1570.0843
1580.138
1590.147
160.859
1600.375
1610.529
1620.657
1630.18
1640.0251
1650.848
1660.0349
1670.295
1680.27
1690.327
170.818
180.177
190.755
20.535
200.141
210.634
220.935
230.00734
240.782
250.186
260.738
270.964
280.815
290.0336
30.458
300.557
310.527
320.0429
330.164
340.222
350.607
360.113
370.462
380.694
390.934
40.269
400.00964
410.197
420.978
430.407
440.063
450.191
460.468
470.403
480.424
490.213
50.235
500.906
510.593
520.318
530.0743
540.419
550.0375
560.977
570.538
580.945
590.904
60.956
600.497
610.0817
620.737
630.678
640.807
650.497
660.489
670.218
680.561
690.894
70.0112
700.252
710.0641
720.936
730.372
740.0698
750.188
760.25
770.759
780.315
790.552
80.118
800.0785
810.243
820.0469
830.751
840.274
850.0366
860.665
870.00414
880.82
890.764
90.54
900.0107
910.0451
920.118
930.234
940.328
950.0118
960.366
970.793
980.869
990.613



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: CNhs13496


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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