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FF:11388-118C2: 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 17:06, 29 March 2012


Name:Peripheral Blood Mononuclear Cells, 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 stage46 years old adult
sexmale
age46
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 numberPBMC724
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-Peripheral0.154
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-Basophils0.154
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0482
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-Whole0.186
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-Whole0.525
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: CNhs12002

Jaspar motifP-value
MA0002.27.7141e-12
MA0003.10.508
MA0004.10.79
MA0006.10.594
MA0007.10.505
MA0009.10.0269
MA0014.10.616
MA0017.10.461
MA0018.21.39792e-4
MA0019.10.466
MA0024.10.0201
MA0025.16.51828e-5
MA0027.10.655
MA0028.10.351
MA0029.10.441
MA0030.10.165
MA0031.10.126
MA0035.20.736
MA0038.10.0946
MA0039.20.733
MA0040.10.565
MA0041.10.805
MA0042.10.859
MA0043.11.7298e-8
MA0046.10.0375
MA0047.20.794
MA0048.10.567
MA0050.14.14919e-9
MA0051.10.00114
MA0052.10.127
MA0055.10.283
MA0057.10.246
MA0058.10.708
MA0059.10.849
MA0060.13.74263e-7
MA0061.13.58033e-24
MA0062.25.95825e-5
MA0065.20.417
MA0066.10.0715
MA0067.15.16598e-5
MA0068.10.377
MA0069.10.741
MA0070.10.0407
MA0071.10.461
MA0072.10.506
MA0073.10.0872
MA0074.10.203
MA0076.10.681
MA0077.10.111
MA0078.10.66
MA0079.20.627
MA0080.21.84477e-15
MA0081.12.15211e-4
MA0083.10.131
MA0084.10.727
MA0087.10.797
MA0088.10.354
MA0090.10.00808
MA0091.10.504
MA0092.10.997
MA0093.10.939
MA0099.21.13561e-29
MA0100.10.473
MA0101.12.5533e-21
MA0102.26.20072e-11
MA0103.10.236
MA0104.20.539
MA0105.12.76981e-15
MA0106.10.0854
MA0107.11.79788e-25
MA0108.20.00531
MA0111.10.483
MA0112.20.112
MA0113.10.294
MA0114.10.861
MA0115.10.204
MA0116.10.00297
MA0117.10.00605
MA0119.10.698
MA0122.10.974
MA0124.10.79
MA0125.10.0854
MA0131.10.794
MA0135.10.419
MA0136.11.09924e-19
MA0137.20.557
MA0138.20.166
MA0139.10.897
MA0140.10.72
MA0141.10.62
MA0142.10.38
MA0143.10.149
MA0144.10.196
MA0145.10.575
MA0146.10.171
MA0147.10.689
MA0148.10.847
MA0149.10.748
MA0150.13.79299e-11
MA0152.10.0662
MA0153.10.00287
MA0154.19.45647e-4
MA0155.10.821
MA0156.14.3765e-18
MA0157.10.188
MA0159.10.191
MA0160.10.168
MA0162.10.332
MA0163.12.68095e-4
MA0164.10.615
MA0258.10.0741
MA0259.10.613



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: CNhs12002

Novel motifP-value
10.471
100.0141
1000.545
1010.796
1020.784
1030.66
1040.503
1050.0937
1065.49434e-4
1070.959
1080.649
1090.26
110.324
1100.913
1110.12
1120.508
1130.0883
1140.208
1150.307
1160.659
1170.0171
1180.268
1190.624
120.242
1200.749
1210.374
1220.281
1230.00893
1240.548
1250.531
1260.206
1270.526
1280.0741
1290.886
130.492
1300.338
1310.679
1320.103
1330.599
1340.809
1350.548
1360.945
1370.00499
1380.211
1390.0359
140.326
1400.3
1410.615
1420.359
1430.00192
1440.596
1450.664
1460.72
1470.16
1480.066
1490.716
150.173
1500.686
1510.141
1520.255
1530.665
1540.352
1550.201
1560.77
1570.952
1580.0308
1590.164
160.982
1600.796
1610.499
1620.0537
1630.346
1640.0632
1650.372
1660.547
1670.319
1680.0126
1690.376
170.442
180.349
190.528
20.853
200.465
210.81
220.513
230.129
240.689
250.199
260.382
270.841
280.367
290.123
30.319
300.309
310.931
320.0195
330.511
340.697
350.0997
360.26
370.18
380.593
390.941
40.996
400.653
410.00988
420.372
430.0493
440.557
450.926
460.411
470.825
480.718
490.14
50.329
500.769
510.478
520.546
530.175
540.592
550.924
560.831
570.892
580.103
590.339
60.92
600.0903
610.183
620.0818
630.889
640.464
650.351
660.0404
670.454
680.208
690.428
70.343
700.13
710.0908
720.184
730.219
740.225
750.109
760.123
770.805
780.255
790.912
80.752
800.023
810.44
820.175
830.678
840.0435
850.0964
860.0158
870.398
880.712
890.597
90.318
900.203
910.484
920.338
930.753
940.138
950.14
960.712
970.966
980.168
999.43601e-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: CNhs12002


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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