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FF:11312-117C7: 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 17:03, 29 March 2012


Name:Peripheral Blood Mononuclear Cells, 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 stage65 years old adult
sexmale
age65
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 numberPBMC722
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-Peripheral0.169
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-Basophils0.156
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0776
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
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-Whole0.318
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-Whole0.361
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: CNhs11958

Jaspar motifP-value
MA0002.29.79905e-12
MA0003.10.533
MA0004.10.875
MA0006.10.652
MA0007.10.988
MA0009.10.0943
MA0014.10.871
MA0017.10.639
MA0018.21.79131e-5
MA0019.10.231
MA0024.10.03
MA0025.14.4327e-4
MA0027.10.781
MA0028.10.408
MA0029.10.201
MA0030.10.0979
MA0031.10.0456
MA0035.20.538
MA0038.10.106
MA0039.20.675
MA0040.10.494
MA0041.10.4
MA0042.10.801
MA0043.11.17252e-10
MA0046.10.00626
MA0047.20.67
MA0048.10.848
MA0050.13.15319e-7
MA0051.10.00776
MA0052.10.286
MA0055.10.644
MA0057.10.352
MA0058.10.827
MA0059.10.814
MA0060.14.56945e-8
MA0061.11.54218e-18
MA0062.20.00154
MA0065.20.231
MA0066.10.092
MA0067.15.59294e-5
MA0068.10.0684
MA0069.10.806
MA0070.10.00841
MA0071.10.296
MA0072.10.586
MA0073.10.218
MA0074.10.207
MA0076.10.661
MA0077.10.136
MA0078.10.815
MA0079.20.542
MA0080.21.76231e-15
MA0081.11.56452e-4
MA0083.10.289
MA0084.10.491
MA0087.10.752
MA0088.10.558
MA0090.10.0144
MA0091.10.63
MA0092.10.927
MA0093.10.951
MA0099.24.04566e-20
MA0100.10.522
MA0101.11.12031e-16
MA0102.21.84424e-10
MA0103.10.28
MA0104.20.538
MA0105.13.24724e-18
MA0106.10.135
MA0107.12.20805e-19
MA0108.20.00272
MA0111.10.358
MA0112.20.01
MA0113.10.473
MA0114.10.925
MA0115.10.181
MA0116.17.56885e-4
MA0117.10.0178
MA0119.10.764
MA0122.10.782
MA0124.10.558
MA0125.10.0266
MA0131.10.894
MA0135.10.871
MA0136.12.77941e-19
MA0137.20.919
MA0138.20.0911
MA0139.10.762
MA0140.10.441
MA0141.10.376
MA0142.10.483
MA0143.10.487
MA0144.10.35
MA0145.10.959
MA0146.10.106
MA0147.10.633
MA0148.10.754
MA0149.10.624
MA0150.15.00889e-10
MA0152.10.0696
MA0153.10.00168
MA0154.10.00231
MA0155.10.987
MA0156.19.93405e-16
MA0157.10.0557
MA0159.10.0473
MA0160.10.121
MA0162.10.978
MA0163.17.29321e-7
MA0164.10.797
MA0258.10.0263
MA0259.10.854



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: CNhs11958

Novel motifP-value
10.281
100.0134
1000.992
1010.635
1020.932
1030.721
1040.574
1050.108
1060.00229
1070.836
1080.668
1090.251
110.254
1100.557
1110.11
1120.567
1130.12
1140.133
1150.28
1160.784
1170.00966
1180.153
1190.677
120.295
1200.602
1210.669
1220.51
1234.80821e-4
1240.929
1250.427
1260.328
1270.793
1280.0893
1290.823
130.272
1300.228
1310.694
1320.0918
1330.769
1340.839
1350.533
1360.999
1370.00179
1380.178
1390.0229
140.32
1400.499
1410.368
1420.758
1430.0105
1440.59
1450.655
1460.607
1470.196
1480.0648
1490.818
150.116
1500.768
1510.15
1520.382
1530.887
1540.357
1550.314
1560.829
1570.808
1580.0673
1590.0421
160.823
1600.965
1610.58
1620.0933
1630.624
1640.0555
1650.273
1660.777
1670.276
1680.155
1690.109
170.452
180.331
190.995
20.612
200.378
210.768
220.617
230.119
240.814
250.192
260.185
270.972
280.388
290.0907
30.233
300.191
310.969
320.102
330.253
340.815
350.107
360.124
370.127
380.585
390.988
40.832
400.37
410.0135
420.432
430.0459
440.605
450.888
460.306
470.647
480.577
490.0823
50.216
500.792
510.505
520.567
530.138
540.553
550.911
560.803
570.951
580.107
590.466
60.927
600.095
610.254
620.0695
630.78
640.397
650.363
660.0396
670.714
680.386
690.592
70.284
700.0681
710.0485
720.301
730.234
740.183
750.0754
760.0815
770.611
780.264
790.695
80.946
800.0364
810.374
820.129
830.419
840.0907
850.0698
860.0236
870.443
880.785
890.679
90.457
900.134
910.227
920.316
930.866
940.0846
950.189
960.476
970.987
980.136
990.00342



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: CNhs11958


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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