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FF:11231-116C7: 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:Peripheral Blood Mononuclear 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 typemononuclear cell
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberPBMC721
catalog number3H100-10-10
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-Basophils0.21
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.159
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-Whole0.21
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-Whole0.424
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: CNhs10860

Jaspar motifP-value
MA0002.22.28745e-10
MA0003.10.859
MA0004.10.952
MA0006.10.337
MA0007.10.432
MA0009.10.0191
MA0014.10.785
MA0017.10.874
MA0018.24.1566e-4
MA0019.10.418
MA0024.10.0498
MA0025.10.00525
MA0027.10.994
MA0028.10.775
MA0029.10.368
MA0030.10.0182
MA0031.10.00332
MA0035.20.98
MA0038.10.242
MA0039.20.742
MA0040.10.568
MA0041.10.414
MA0042.10.92
MA0043.15.03907e-7
MA0046.10.0763
MA0047.20.541
MA0048.10.194
MA0050.11.92324e-8
MA0051.10.00341
MA0052.10.795
MA0055.10.0327
MA0057.10.388
MA0058.10.942
MA0059.10.444
MA0060.12.45221e-4
MA0061.12.4972e-11
MA0062.23.17287e-8
MA0065.20.833
MA0066.10.205
MA0067.14.86575e-4
MA0068.10.688
MA0069.10.43
MA0070.10.0942
MA0071.10.559
MA0072.10.17
MA0073.10.501
MA0074.10.986
MA0076.10.343
MA0077.10.0768
MA0078.10.676
MA0079.20.994
MA0080.22.62743e-16
MA0081.13.38648e-4
MA0083.10.109
MA0084.10.889
MA0087.10.988
MA0088.10.295
MA0090.10.00145
MA0091.10.604
MA0092.10.938
MA0093.10.793
MA0099.22.81434e-5
MA0100.10.935
MA0101.16.84751e-6
MA0102.24.03533e-8
MA0103.10.547
MA0104.20.691
MA0105.11.9261e-8
MA0106.10.0206
MA0107.19.48304e-7
MA0108.21.17482e-4
MA0111.10.354
MA0112.20.359
MA0113.10.447
MA0114.10.509
MA0115.10.138
MA0116.10.0016
MA0117.10.00999
MA0119.10.593
MA0122.10.831
MA0124.10.7
MA0125.10.114
MA0131.10.834
MA0135.10.657
MA0136.17.68459e-22
MA0137.20.944
MA0138.20.142
MA0139.10.984
MA0140.10.584
MA0141.10.612
MA0142.10.374
MA0143.10.437
MA0144.10.57
MA0145.10.49
MA0146.10.371
MA0147.10.836
MA0148.10.782
MA0149.10.721
MA0150.17.92109e-5
MA0152.10.0246
MA0153.10.0126
MA0154.10.0167
MA0155.10.601
MA0156.19.74992e-20
MA0157.10.0146
MA0159.10.195
MA0160.10.507
MA0162.10.209
MA0163.12.23748e-4
MA0164.10.981
MA0258.10.196
MA0259.10.74



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: CNhs10860

Novel motifP-value
10.443
100.0148
1000.443
1010.428
1020.711
1030.6
1040.592
1050.167
1060.00995
1070.558
1080.475
1090.423
110.378
1100.884
1110.14
1120.613
1130.0422
1140.205
1150.152
1160.321
1170.0177
1180.326
1190.974
120.399
1200.322
1210.472
1220.359
1230.00346
1240.364
1250.796
1260.206
1270.413
1280.234
1290.752
130.693
1300.244
1310.683
1320.108
1330.474
1340.879
1350.31
1360.635
1375.08791e-4
1380.113
1390.0118
140.28
1400.424
1410.511
1420.941
1430.00588
1440.75
1450.986
1460.816
1470.0353
1480.195
1490.647
150.116
1500.907
1510.216
1520.955
1530.706
1540.291
1550.0682
1560.561
1570.899
1580.00548
1590.754
160.859
1600.479
1610.78
1620.0556
1630.776
1640.252
1650.229
1660.613
1670.453
1680.154
1690.952
170.765
180.566
190.399
20.846
200.748
210.75
220.948
230.211
240.432
250.0972
260.643
270.556
280.359
290.233
30.32
300.227
310.997
320.0196
330.454
340.886
350.153
360.208
370.359
380.675
390.662
40.804
400.871
410.034
420.278
430.117
440.593
450.739
460.451
470.679
480.646
490.107
50.211
500.656
510.541
520.757
530.103
540.627
550.824
560.849
570.94
580.0493
590.962
60.845
600.138
610.133
620.033
630.945
640.516
650.569
660.214
670.818
680.329
690.734
70.333
700.0782
710.0982
720.232
730.671
740.159
750.0836
760.119
770.169
780.341
790.857
80.662
800.0102
810.436
820.223
830.913
840.252
850.181
860.0469
870.812
880.604
890.215
90.447
900.0291
910.431
920.288
930.572
940.122
950.37
960.86
970.733
980.302
993.62659e-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: CNhs10860


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)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000842 (mononuclear cell)
0000988 (hematopoietic cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002384 (connective tissue)
0002390 (hematopoietic system)
0004535 (cardiovascular system)

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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