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FF:11230-116C6: 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 16:35, 29 March 2012


Name:Natural Killer Cells, donor1
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 stage47 years old adult
sexmale
age47
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 numberNK725
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-Peripheral0.0781
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-Basophils0.202
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.128
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
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-Whole0.758
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: CNhs10859

Jaspar motifP-value
MA0002.21.51098e-7
MA0003.10.488
MA0004.10.948
MA0006.10.189
MA0007.10.314
MA0009.10.00446
MA0014.10.841
MA0017.10.132
MA0018.23.04124e-10
MA0019.10.77
MA0024.10.677
MA0025.10.00471
MA0027.10.699
MA0028.10.00393
MA0029.10.584
MA0030.10.00253
MA0031.16.62906e-5
MA0035.20.67
MA0038.10.268
MA0039.20.423
MA0040.10.848
MA0041.10.305
MA0042.10.824
MA0043.12.18678e-8
MA0046.10.0425
MA0047.20.546
MA0048.10.954
MA0050.11.6634e-10
MA0051.12.18228e-4
MA0052.10.336
MA0055.10.527
MA0057.10.136
MA0058.10.937
MA0059.10.511
MA0060.10.174
MA0061.11.24487e-20
MA0062.22.86028e-15
MA0065.20.812
MA0066.10.486
MA0067.15.07221e-5
MA0068.10.807
MA0069.10.826
MA0070.10.343
MA0071.10.733
MA0072.10.00218
MA0073.10.535
MA0074.10.765
MA0076.10.00101
MA0077.10.284
MA0078.10.91
MA0079.20.835
MA0080.25.04126e-13
MA0081.14.01043e-4
MA0083.10.282
MA0084.10.14
MA0087.10.729
MA0088.10.202
MA0090.12.49064e-4
MA0091.10.257
MA0092.10.828
MA0093.10.865
MA0099.23.0888e-6
MA0100.10.561
MA0101.11.13079e-15
MA0102.20.00372
MA0103.10.155
MA0104.20.751
MA0105.14.2297e-11
MA0106.10.027
MA0107.11.42638e-15
MA0108.20.00567
MA0111.10.361
MA0112.20.157
MA0113.10.248
MA0114.10.131
MA0115.10.0568
MA0116.10.155
MA0117.10.0035
MA0119.10.173
MA0122.10.932
MA0124.10.209
MA0125.10.0739
MA0131.10.106
MA0135.10.255
MA0136.11.29e-21
MA0137.20.952
MA0138.20.00662
MA0139.10.952
MA0140.10.969
MA0141.10.101
MA0142.10.174
MA0143.10.139
MA0144.10.927
MA0145.10.0948
MA0146.11
MA0147.10.818
MA0148.10.643
MA0149.10.934
MA0150.10.00229
MA0152.10.0154
MA0153.10.0504
MA0154.10.677
MA0155.10.142
MA0156.19.86036e-19
MA0157.10.00628
MA0159.10.804
MA0160.10.911
MA0162.10.183
MA0163.10.0429
MA0164.10.803
MA0258.10.56
MA0259.10.868



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: CNhs10859

Novel motifP-value
10.904
100.0169
1000.792
1010.56
1020.992
1030.798
1040.694
1050.402
1060.25
1070.038
1080.36
1090.857
110.891
1100.36
1110.536
1120.896
1130.277
1140.934
1150.215
1160.112
1170.0134
1180.469
1190.333
120.371
1200.192
1210.392
1220.648
1230.00365
1240.944
1250.593
1260.442
1270.764
1280.884
1290.252
130.5
1300.262
1310.273
1320.0845
1330.471
1340.831
1350.679
1360.874
1370.0231
1380.479
1390.18
140.475
1400.733
1410.875
1420.519
1430.00909
1440.879
1450.543
1460.551
1470.0226
1480.542
1490.121
150.301
1500.991
1510.443
1520.841
1530.893
1540.249
1550.101
1560.694
1570.687
1580.0133
1590.609
160.287
1600.0307
1610.924
1620.00736
1630.897
1640.173
1650.632
1660.572
1670.214
1680.719
1690.211
170.708
180.846
190.0298
20.139
200.178
210.551
220.314
230.994
240.776
250.189
260.763
270.489
280.394
290.128
30.729
300.0921
310.632
320.00241
330.365
340.518
350.431
360.0986
370.498
380.709
390.478
40.765
400.919
410.0387
420.544
430.445
440.492
450.163
460.911
470.963
480.864
490.285
50.482
500.523
510.922
520.869
530.357
540.968
550.313
560.776
570.614
580.206
590.189
60.774
600.521
610.326
620.335
630.637
640.912
650.561
660.447
670.615
680.606
690.576
70.559
700.28
710.24
720.24
730.528
740.952
750.0731
760.132
770.00315
780.983
790.893
80.215
800.00856
810.971
820.667
830.59
840.147
850.761
860.0495
870.894
880.725
890.00789
90.965
900.833
910.703
920.586
930.656
940.222
950.289
960.934
970.559
980.597
994.34782e-7



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: CNhs10859


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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