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FF:11624-122B4: 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 17:17, 29 March 2012


Name:CD19+ B 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 stageNA
sexNA
ageNA
cell typeb cell
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number3H100-500-10
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-penis0
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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
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: CNhs12352

Jaspar motifP-value
MA0002.20.0011
MA0003.10.693
MA0004.10.477
MA0006.10.179
MA0007.10.446
MA0009.10.22
MA0014.10.858
MA0017.10.773
MA0018.21.02908e-9
MA0019.10.556
MA0024.10.636
MA0025.10.214
MA0027.10.83
MA0028.10.767
MA0029.10.285
MA0030.10.00845
MA0031.10.0171
MA0035.20.922
MA0038.10.0463
MA0039.20.389
MA0040.10.527
MA0041.10.161
MA0042.10.707
MA0043.15.09512e-5
MA0046.10.144
MA0047.20.567
MA0048.10.819
MA0050.15.41809e-9
MA0051.10.00169
MA0052.10.174
MA0055.10.89
MA0057.10.203
MA0058.10.38
MA0059.10.696
MA0060.14.64828e-4
MA0061.11.59651e-21
MA0062.21.59816e-4
MA0065.20.503
MA0066.10.447
MA0067.17.00939e-4
MA0068.10.269
MA0069.10.67
MA0070.10.155
MA0071.10.985
MA0072.10.886
MA0073.10.567
MA0074.10.999
MA0076.10.505
MA0077.10.252
MA0078.10.967
MA0079.20.628
MA0080.28.11542e-12
MA0081.13.86031e-4
MA0083.10.0828
MA0084.10.801
MA0087.10.37
MA0088.10.143
MA0090.14.39753e-5
MA0091.10.627
MA0092.10.971
MA0093.10.63
MA0099.20.896
MA0100.10.665
MA0101.11.29945e-19
MA0102.20.00152
MA0103.10.165
MA0104.20.106
MA0105.11.10355e-15
MA0106.10.189
MA0107.11.2612e-19
MA0108.20.00155
MA0111.10.38
MA0112.20.482
MA0113.10.182
MA0114.10.763
MA0115.10.426
MA0116.10.00331
MA0117.10.0313
MA0119.10.354
MA0122.10.932
MA0124.10.97
MA0125.10.119
MA0131.10.1
MA0135.10.0742
MA0136.12.37049e-13
MA0137.20.0167
MA0138.20.0911
MA0139.10.701
MA0140.10.946
MA0141.10.386
MA0142.10.668
MA0143.10.672
MA0144.10.0969
MA0145.10.0609
MA0146.10.479
MA0147.10.157
MA0148.10.519
MA0149.10.439
MA0150.10.137
MA0152.10.0666
MA0153.10.0117
MA0154.10.00219
MA0155.10.476
MA0156.11.46389e-5
MA0157.10.0448
MA0159.10.148
MA0160.10.79
MA0162.10.347
MA0163.14.69227e-4
MA0164.10.256
MA0258.10.184
MA0259.10.598



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: CNhs12352

Novel motifP-value
10.389
100.00751
1000.578
1010.41
1020.958
1030.871
1040.631
1050.754
1060.0108
1070.425
1080.343
1090.885
110.442
1100.823
1110.13
1120.599
1130.0466
1140.555
1150.868
1160.38
1170.00207
1180.199
1190.918
120.475
1200.321
1210.26
1220.616
1231.43183e-4
1240.973
1250.371
1260.404
1270.787
1280.887
1290.278
130.501
1300.0459
1310.526
1320.0724
1330.011
1340.656
1350.0636
1360.652
1370.00888
1380.511
1390.278
140.461
1400.326
1410.189
1420.722
1430.44
1440.787
1450.894
1460.658
1470.134
1480.102
1490.866
150.335
1500.561
1510.828
1520.83
1530.469
1540.28
1550.0334
1560.687
1570.587
1580.00505
1590.308
160.467
1600.597
1610.711
1620.171
1630.291
1640.0531
1650.697
1660.595
1670.105
1680.662
1690.711
170.915
180.685
190.224
20.259
200.153
210.859
220.426
230.812
240.795
250.0923
260.346
270.648
280.482
290.104
30.431
300.0832
310.83
320.0141
330.443
340.561
350.118
360.0457
370.255
380.79
390.603
40.865
400.484
410.0612
420.404
430.179
440.965
450.403
460.401
470.549
480.784
490.0765
50.828
500.795
510.721
520.755
530.396
540.998
550.747
560.769
570.757
580.0629
590.948
60.802
600.305
610.0969
620.106
631
640.652
650.937
660.171
670.895
680.445
690.598
70.39
700.173
710.0638
720.256
730.51
740.813
750.0166
760.0157
770.0397
780.628
790.609
80.79
800.196
810.289
820.213
830.441
840.0292
850.212
860.0378
870.574
880.701
890.0318
90.93
900.121
910.0744
920.665
930.98
940.143
950.157
960.804
970.548
980.12
991.28154e-5



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: CNhs12352


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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