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FF:11311-117C6: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:03, 29 March 2012


Name:Natural Killer Cells, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stage57 years old adult
sexmale
age57
cell typenatural killer cell
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNK726
catalog number3H100-50-10
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Basophils0.217
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0848
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C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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-Whole0.725
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: CNhs11957

Jaspar motifP-value
MA0002.24.49468e-6
MA0003.10.342
MA0004.10.771
MA0006.10.25
MA0007.10.326
MA0009.10.0118
MA0014.10.676
MA0017.10.069
MA0018.22.87007e-10
MA0019.10.724
MA0024.10.753
MA0025.10.135
MA0027.10.501
MA0028.10.0456
MA0029.10.649
MA0030.10.014
MA0031.11.06832e-4
MA0035.20.618
MA0038.10.0481
MA0039.20.217
MA0040.10.743
MA0041.10.247
MA0042.10.634
MA0043.11.82964e-4
MA0046.10.0284
MA0047.20.688
MA0048.10.56
MA0050.12.4198e-6
MA0051.10.0224
MA0052.10.0564
MA0055.10.662
MA0057.10.166
MA0058.10.741
MA0059.10.57
MA0060.10.0551
MA0061.11.58873e-16
MA0062.25.86746e-10
MA0065.20.86
MA0066.10.619
MA0067.17.22827e-4
MA0068.10.605
MA0069.10.963
MA0070.10.448
MA0071.10.718
MA0072.10.0435
MA0073.10.547
MA0074.10.909
MA0076.10.0225
MA0077.10.147
MA0078.10.876
MA0079.20.783
MA0080.23.15123e-10
MA0081.10.0102
MA0083.10.478
MA0084.10.254
MA0087.10.5
MA0088.10.206
MA0090.11.58917e-4
MA0091.10.251
MA0092.10.76
MA0093.10.668
MA0099.20.17
MA0100.10.966
MA0101.15.29404e-12
MA0102.20.582
MA0103.10.503
MA0104.20.861
MA0105.12.26145e-11
MA0106.10.057
MA0107.12.20756e-11
MA0108.24.52069e-4
MA0111.10.331
MA0112.20.22
MA0113.10.239
MA0114.10.154
MA0115.10.0964
MA0116.10.111
MA0117.10.0119
MA0119.10.327
MA0122.10.707
MA0124.10.0671
MA0125.10.068
MA0131.10.0599
MA0135.10.138
MA0136.14.11708e-15
MA0137.20.203
MA0138.20.0283
MA0139.10.93
MA0140.10.97
MA0141.10.176
MA0142.10.0904
MA0143.10.0955
MA0144.10.538
MA0145.10.0288
MA0146.10.592
MA0147.10.829
MA0148.10.979
MA0149.10.772
MA0150.10.0779
MA0152.10.00683
MA0153.10.0658
MA0154.10.986
MA0155.10.182
MA0156.17.68695e-11
MA0157.10.00692
MA0159.10.925
MA0160.10.888
MA0162.10.293
MA0163.10.025
MA0164.10.52
MA0258.10.855
MA0259.10.739



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: CNhs11957

Novel motifP-value
10.994
100.00862
1000.688
1010.341
1020.939
1030.512
1040.791
1050.718
1060.159
1070.0806
1080.613
1090.894
110.835
1100.417
1110.554
1120.832
1130.178
1140.94
1150.385
1160.175
1170.0075
1180.41
1190.575
120.651
1200.269
1210.454
1220.889
1234.95687e-6
1240.808
1250.643
1260.684
1270.301
1280.911
1290.182
130.508
1300.238
1310.405
1320.196
1330.276
1340.771
1350.292
1360.784
1370.0754
1380.842
1390.202
140.453
1400.737
1410.725
1420.248
1430.0375
1440.936
1450.708
1460.413
1470.0301
1480.415
1490.184
150.325
1500.975
1510.366
1520.994
1530.483
1540.102
1550.0628
1560.672
1570.773
1580.023
1590.405
160.209
1600.0524
1610.639
1620.0332
1630.753
1640.0758
1650.766
1660.422
1670.106
1680.504
1690.304
170.7
180.725
190.0676
20.108
200.111
210.896
220.221
230.901
240.455
250.175
260.936
270.422
280.344
290.118
30.669
300.046
310.562
320.0186
330.503
340.297
350.373
360.114
370.45
380.633
390.519
40.974
400.928
410.159
420.506
430.546
440.597
450.0982
460.998
470.876
480.923
490.183
50.614
500.44
510.947
520.865
530.224
540.977
550.538
560.798
570.88
580.178
590.19
60.937
600.581
610.309
620.331
630.749
640.912
650.539
660.271
670.44
680.769
690.934
70.686
700.292
710.238
720.441
730.424
740.627
750.0412
760.0946
770.00238
780.859
790.535
80.267
800.086
810.887
820.694
830.787
840.066
850.704
860.0354
870.976
880.901
890.00379
90.764
900.911
910.748
920.971
930.834
940.325
950.156
960.837
970.266
980.608
996.69795e-6



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: CNhs11957


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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000623 (natural killer cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000825 (pro-NK cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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