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FF:11309-117C4: 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 17:13, 29 March 2012


Name:Dendritic Cells - plasmacytoid, 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 stage25 years old adult
sexmale
age25
cell typedendritic cell, plasmacytoid
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberPDC738
catalog number3H100-72-5
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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.203
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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
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: CNhs12196

Jaspar motifP-value
MA0002.22.54078e-8
MA0003.10.368
MA0004.10.346
MA0006.10.539
MA0007.10.733
MA0009.10.131
MA0014.10.819
MA0017.10.572
MA0018.20.00174
MA0019.10.489
MA0024.10.216
MA0025.10.00678
MA0027.10.345
MA0028.10.0257
MA0029.10.53
MA0030.10.146
MA0031.10.0895
MA0035.20.806
MA0038.10.525
MA0039.20.544
MA0040.10.0743
MA0041.10.401
MA0042.10.158
MA0043.10.00256
MA0046.10.713
MA0047.20.416
MA0048.12.469e-4
MA0050.18.53609e-9
MA0051.14.02508e-5
MA0052.10.0124
MA0055.12.38659e-5
MA0057.10.286
MA0058.10.132
MA0059.10.477
MA0060.10.352
MA0061.17.585e-13
MA0062.21.67708e-12
MA0065.20.0555
MA0066.10.198
MA0067.10.0017
MA0068.10.415
MA0069.10.52
MA0070.10.397
MA0071.10.863
MA0072.10.521
MA0073.10.284
MA0074.10.892
MA0076.10.00106
MA0077.10.314
MA0078.10.978
MA0079.20.449
MA0080.23.86085e-13
MA0081.16.94711e-6
MA0083.10.229
MA0084.10.192
MA0087.10.501
MA0088.10.825
MA0090.12.0366e-4
MA0091.10.0121
MA0092.10.891
MA0093.10.349
MA0099.27.96107e-5
MA0100.10.489
MA0101.13.86269e-13
MA0102.20.0177
MA0103.10.0303
MA0104.20.0689
MA0105.14.38539e-10
MA0106.10.0898
MA0107.11.53274e-13
MA0108.20.0212
MA0111.10.553
MA0112.20.0904
MA0113.10.852
MA0114.10.74
MA0115.10.262
MA0116.10.00179
MA0117.10.0596
MA0119.10.641
MA0122.10.218
MA0124.10.665
MA0125.10.431
MA0131.10.613
MA0135.10.592
MA0136.15.75089e-15
MA0137.20.991
MA0138.20.955
MA0139.10.993
MA0140.10.622
MA0141.10.896
MA0142.10.877
MA0143.10.861
MA0144.10.711
MA0145.10.418
MA0146.10.158
MA0147.10.139
MA0148.10.605
MA0149.10.93
MA0150.10.00165
MA0152.10.116
MA0153.10.0489
MA0154.10.00248
MA0155.10.755
MA0156.15.89353e-12
MA0157.10.209
MA0159.10.299
MA0160.10.577
MA0162.10.73
MA0163.14.94958e-6
MA0164.10.823
MA0258.10.167
MA0259.10.462



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: CNhs12196

Novel motifP-value
10.625
100.0455
1000.561
1010.666
1020.59
1030.0512
1040.646
1050.411
1060.0432
1070.347
1080.147
1090.155
110.27
1100.692
1110.736
1120.906
1130.687
1140.499
1150.493
1160.345
1170.00532
1180.58
1190.302
120.426
1200.439
1210.552
1220.239
1230.827
1240.0909
1250.347
1260.129
1270.405
1280.374
1290.369
130.0945
1300.619
1310.648
1320.0123
1330.0959
1340.512
1350.417
1360.686
1370.00167
1380.915
1390.141
140.266
1400.624
1410.582
1420.288
1430.00145
1440.867
1450.52
1460.591
1470.122
1480.0814
1490.361
150.0833
1500.579
1510.314
1520.749
1530.386
1540.992
1550.141
1560.659
1570.734
1580.378
1590.191
160.559
1600.475
1610.208
1620.215
1630.986
1640.563
1650.409
1660.472
1670.547
1680.828
1690.958
170.966
180.528
190.389
20.832
200.5
210.939
220.56
230.596
240.388
250.11
260.932
270.0991
280.363
290.0179
30.19
300.464
310.587
320.0782
330.258
340.918
350.0725
360.143
370.0764
380.513
390.541
40.227
400.587
410.051
420.115
430.199
440.821
450.813
460.382
470.481
480.715
490.278
50.43
500.697
510.266
520.757
530.603
540.824
550.449
560.707
570.938
580.0361
590.457
60.955
600.193
610.146
620.022
630.913
640.553
650.647
660.68
670.142
680.445
690.581
70.127
700.309
710.0691
720.219
730.258
740.459
750.123
760.577
770.699
780.0676
790.817
80.605
800.0462
810.433
820.239
830.297
840.269
850.392
860.0257
870.0575
880.286
890.709
90.414
900.104
910.899
920.633
930.821
940.138
950.014
960.806
970.931
980.112
994.0805e-4



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: CNhs12196


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000451 (dendritic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000784 (plasmacytoid dendritic cell)
0000988 (hematopoietic cell)
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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