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FF:12189-129B2: 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 17:12, 29 March 2012


Name:CD19+ B Cells (pluriselect), donor090309, donation1
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 stageNA
sexNA
ageNA
cell typeb cell
cell lineNA
companyNA
collaborationMatched_genome_OSC(contact:Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-0.126
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.245
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs12177

Jaspar motifP-value
MA0002.24.30773e-7
MA0003.10.431
MA0004.10.403
MA0006.10.626
MA0007.10.801
MA0009.10.945
MA0014.10.828
MA0017.10.0194
MA0018.20.937
MA0019.10.822
MA0024.10.479
MA0025.10.343
MA0027.10.578
MA0028.10.0091
MA0029.10.854
MA0030.10.0625
MA0031.10.233
MA0035.20.148
MA0038.10.348
MA0039.20.864
MA0040.10.708
MA0041.10.134
MA0042.10.769
MA0043.10.856
MA0046.10.767
MA0047.20.145
MA0048.10.297
MA0050.15.0443e-9
MA0051.12.00821e-4
MA0052.10.335
MA0055.10.815
MA0057.10.922
MA0058.10.35
MA0059.10.195
MA0060.10.255
MA0061.14.29804e-4
MA0062.23.7232e-8
MA0065.20.0131
MA0066.10.118
MA0067.10.708
MA0068.10.367
MA0069.10.344
MA0070.10.512
MA0071.10.528
MA0072.10.418
MA0073.10.744
MA0074.10.653
MA0076.10.00119
MA0077.10.564
MA0078.10.774
MA0079.20.356
MA0080.22.70075e-11
MA0081.10.00161
MA0083.10.139
MA0084.10.294
MA0087.10.359
MA0088.10.135
MA0090.17.88899e-4
MA0091.10.216
MA0092.10.768
MA0093.10.513
MA0099.20.0857
MA0100.10.442
MA0101.10.0564
MA0102.20.923
MA0103.10.0143
MA0104.20.127
MA0105.11.61476e-7
MA0106.10.995
MA0107.10.0243
MA0108.21.06069e-6
MA0111.10.452
MA0112.20.00105
MA0113.10.288
MA0114.10.0535
MA0115.10.217
MA0116.18.5076e-6
MA0117.10.845
MA0119.10.957
MA0122.10.432
MA0124.10.884
MA0125.10.669
MA0131.10.355
MA0135.10.0158
MA0136.11.07114e-14
MA0137.20.742
MA0138.20.267
MA0139.10.209
MA0140.10.0156
MA0141.10.501
MA0142.10.0358
MA0143.10.5
MA0144.10.952
MA0145.10.784
MA0146.10.37
MA0147.10.123
MA0148.10.281
MA0149.10.0591
MA0150.10.962
MA0152.10.331
MA0153.10.0393
MA0154.12.39889e-4
MA0155.10.886
MA0156.17.79553e-10
MA0157.10.121
MA0159.10.0356
MA0160.10.3
MA0162.10.568
MA0163.17.6575e-11
MA0164.10.979
MA0258.10.0108
MA0259.10.542



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: CNhs12177

Novel motifP-value
10.106
100.054
1000.602
1010.311
1020.99
1030.0546
1040.215
1050.213
1060.194
1070.947
1080.362
1090.058
110.0492
1100.14
1110.113
1120.221
1130.0471
1140.155
1150.702
1160.958
1170.0083
1180.26
1190.469
120.792
1200.388
1210.962
1220.616
1230.148
1240.03
1250.127
1260.124
1270.479
1280.703
1290.643
130.528
1300.459
1310.511
1320.579
1330.0108
1340.731
1350.796
1360.897
1370.182
1380.475
1390.045
140.434
1400.177
1410.0454
1420.485
1430.00538
1440.849
1450.269
1460.107
1470.203
1480.226
1490.172
150.0737
1500.51
1510.622
1520.983
1530.722
1540.987
1550.0273
1560.573
1570.266
1580.168
1590.102
160.619
1600.296
1610.0999
1620.964
1630.528
1640.646
1650.482
1660.703
1670.0573
1680.0533
1690.23
170.507
180.291
190.993
20.806
200.87
210.742
220.583
230.808
240.297
250.0491
260.132
270.145
280.53
290.141
30.0526
300.624
310.515
320.973
330.472
340.746
350.135
360.00986
370.11
380.359
390.756
40.469
400.115
410.121
420.175
430.0993
440.334
450.742
460.128
470.0695
480.123
490.0776
50.272
500.911
510.349
520.863
530.459
540.572
550.055
560.578
570.217
580.0207
590.208
60.943
600.266
610.0577
620.012
630.497
640.175
650.463
660.548
670.431
680.217
690.843
70.166
700.0315
710.0403
720.0966
730.532
740.126
750.0226
760.26
770.788
780.168
790.296
80.326
800.00748
810.186
820.0823
830.564
840.512
850.402
860.117
870.322
880.954
890.409
90.399
900.0128
910.463
920.509
930.781
940.0409
950.016
960.33
970.505
980.183
990.27



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: CNhs12177


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)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000236 (B cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
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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