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FF:11385-118B8: 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 17:14, 29 March 2012


Name:Dendritic Cells - plasmacytoid, donor3
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 stage24 years old adult
sexfemale
age24
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 numberPDC739
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-0.197
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: CNhs12200

Jaspar motifP-value
MA0002.21.08811e-8
MA0003.10.671
MA0004.10.466
MA0006.10.488
MA0007.10.393
MA0009.10.338
MA0014.10.895
MA0017.10.974
MA0018.25.34024e-4
MA0019.10.595
MA0024.10.413
MA0025.10.0106
MA0027.10.304
MA0028.10.00133
MA0029.10.529
MA0030.10.14
MA0031.10.0553
MA0035.20.656
MA0038.10.234
MA0039.20.956
MA0040.10.511
MA0041.10.346
MA0042.10.142
MA0043.10.00692
MA0046.10.668
MA0047.20.576
MA0048.14.02204e-5
MA0050.16.50698e-4
MA0051.10.0343
MA0052.10.0111
MA0055.15.72061e-6
MA0057.10.343
MA0058.10.214
MA0059.10.636
MA0060.10.289
MA0061.13.23577e-11
MA0062.21.31544e-16
MA0065.20.234
MA0066.10.317
MA0067.17.12581e-4
MA0068.10.184
MA0069.10.616
MA0070.10.312
MA0071.10.976
MA0072.10.442
MA0073.10.236
MA0074.10.92
MA0076.16.16525e-6
MA0077.10.14
MA0078.10.877
MA0079.20.42
MA0080.29.99824e-13
MA0081.11.64643e-5
MA0083.10.1
MA0084.10.247
MA0087.10.708
MA0088.10.892
MA0090.13.50909e-4
MA0091.10.012
MA0092.10.981
MA0093.10.475
MA0099.20.00419
MA0100.10.42
MA0101.16.40172e-11
MA0102.20.0251
MA0103.10.0215
MA0104.20.082
MA0105.11.38635e-7
MA0106.10.069
MA0107.16.89966e-11
MA0108.20.00141
MA0111.10.476
MA0112.20.392
MA0113.10.501
MA0114.10.71
MA0115.10.207
MA0116.10.0164
MA0117.10.0869
MA0119.10.278
MA0122.10.113
MA0124.10.847
MA0125.10.809
MA0131.10.763
MA0135.10.22
MA0136.11.58433e-16
MA0137.20.865
MA0138.20.652
MA0139.10.896
MA0140.10.803
MA0141.10.941
MA0142.10.529
MA0143.10.619
MA0144.10.785
MA0145.10.252
MA0146.10.19
MA0147.10.13
MA0148.10.649
MA0149.10.864
MA0150.10.0153
MA0152.10.1
MA0153.10.0107
MA0154.10.0221
MA0155.10.585
MA0156.13.79679e-14
MA0157.10.203
MA0159.10.327
MA0160.10.597
MA0162.10.395
MA0163.10.00118
MA0164.10.852
MA0258.10.357
MA0259.10.386



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: CNhs12200

Novel motifP-value
10.759
100.0483
1000.572
1010.68
1020.679
1030.0697
1040.459
1050.501
1060.062
1070.4
1080.116
1090.141
110.369
1100.907
1110.55
1120.881
1130.596
1140.384
1150.494
1160.308
1170.0064
1180.43
1190.702
120.407
1200.593
1210.539
1220.156
1230.96
1240.148
1250.252
1260.17
1270.329
1280.368
1290.314
130.104
1300.675
1310.645
1320.0322
1330.238
1340.573
1350.689
1360.771
1370.00188
1380.761
1390.116
140.254
1400.844
1410.438
1420.793
1430.00939
1440.5
1450.539
1460.478
1470.134
1480.121
1490.357
150.1
1500.532
1510.446
1520.787
1530.435
1540.955
1550.0354
1560.916
1570.545
1580.323
1590.248
160.466
1600.309
1610.397
1620.194
1630.712
1640.576
1650.32
1660.281
1670.74
1680.76
1690.701
170.849
180.739
190.229
20.877
200.403
210.983
220.723
230.678
240.229
250.0907
260.989
270.0973
280.286
290.0275
30.323
300.448
310.786
320.0494
330.292
340.906
350.0977
360.187
370.131
380.436
390.414
40.109
400.975
410.0279
420.101
430.286
440.672
450.78
460.578
470.602
480.786
490.292
50.437
500.672
510.339
520.893
530.697
540.997
550.671
560.764
570.858
580.038
590.797
60.796
600.274
610.0772
620.0255
630.956
640.659
650.833
660.577
670.138
680.57
690.539
70.0859
700.0855
710.139
720.154
730.717
740.316
750.154
760.505
770.455
780.018
790.589
80.458
800.00836
810.534
820.277
830.218
840.367
850.543
860.0819
870.0622
880.313
890.63
90.375
900.086
910.982
920.734
930.598
940.255
950.0125
960.932
970.849
980.228
993.77779e-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: CNhs12200


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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