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FF:11544-120B5: 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, 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 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-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
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: CNhs12343

Jaspar motifP-value
MA0002.20.0659
MA0003.10.574
MA0004.10.343
MA0006.10.113
MA0007.10.505
MA0009.10.294
MA0014.10.899
MA0017.10.369
MA0018.25.68517e-11
MA0019.10.718
MA0024.10.627
MA0025.10.486
MA0027.10.751
MA0028.10.124
MA0029.10.407
MA0030.10.0016
MA0031.10.00181
MA0035.20.812
MA0038.10.0225
MA0039.20.582
MA0040.10.496
MA0041.10.174
MA0042.10.781
MA0043.16.55992e-6
MA0046.10.215
MA0047.20.268
MA0048.10.933
MA0050.18.63256e-9
MA0051.10.0023
MA0052.10.064
MA0055.10.495
MA0057.10.213
MA0058.10.248
MA0059.10.775
MA0060.10.0137
MA0061.11.97491e-18
MA0062.26.7264e-7
MA0065.20.912
MA0066.10.8
MA0067.18.44085e-4
MA0068.10.162
MA0069.10.557
MA0070.10.492
MA0071.10.661
MA0072.10.693
MA0073.10.601
MA0074.10.773
MA0076.10.031
MA0077.10.315
MA0078.10.72
MA0079.20.701
MA0080.28.98004e-11
MA0081.16.22175e-5
MA0083.10.422
MA0084.10.446
MA0087.10.298
MA0088.10.335
MA0090.18.77677e-6
MA0091.10.739
MA0092.10.632
MA0093.10.448
MA0099.22.4602e-4
MA0100.10.514
MA0101.12.17999e-15
MA0102.20.067
MA0103.10.152
MA0104.20.0886
MA0105.18.9895e-12
MA0106.10.199
MA0107.17.70744e-15
MA0108.20.00107
MA0111.10.49
MA0112.20.582
MA0113.10.181
MA0114.10.439
MA0115.10.684
MA0116.10.00788
MA0117.10.112
MA0119.10.198
MA0122.10.914
MA0124.10.695
MA0125.10.36
MA0131.10.0143
MA0135.10.031
MA0136.12.05428e-12
MA0137.20.0232
MA0138.20.154
MA0139.10.673
MA0140.10.829
MA0141.10.0972
MA0142.10.782
MA0143.10.368
MA0144.10.0546
MA0145.10.0375
MA0146.10.653
MA0147.10.136
MA0148.10.737
MA0149.10.346
MA0150.10.982
MA0152.10.0649
MA0153.10.0286
MA0154.10.0314
MA0155.10.228
MA0156.14.9152e-6
MA0157.10.056
MA0159.10.369
MA0160.10.797
MA0162.10.228
MA0163.10.00431
MA0164.10.442
MA0258.10.867
MA0259.10.296



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: CNhs12343

Novel motifP-value
10.523
100.0162
1000.408
1010.542
1020.782
1030.443
1040.666
1050.865
1060.163
1070.07
1080.261
1090.974
110.733
1100.736
1110.219
1120.712
1130.0607
1140.875
1150.917
1160.162
1177.95649e-4
1180.238
1190.7
120.695
1200.433
1210.269
1220.727
1235.22776e-4
1240.832
1250.438
1260.443
1270.509
1280.344
1290.135
130.443
1300.0515
1310.41
1320.0832
1330.166
1340.912
1350.0192
1360.355
1370.00732
1380.582
1390.405
140.564
1400.31
1410.448
1420.972
1430.54
1440.619
1450.761
1460.646
1470.0461
1480.24
1490.873
150.681
1500.772
1510.877
1520.803
1530.467
1540.391
1550.0198
1560.782
1570.423
1580.00503
1590.463
160.321
1600.448
1610.854
1620.545
1630.354
1640.0813
1650.906
1660.226
1670.121
1680.44
1690.303
170.66
180.805
190.0923
20.0817
200.102
210.965
220.311
230.833
240.454
250.116
260.659
270.457
280.491
290.0864
30.444
300.0605
310.675
320.0183
330.513
340.389
350.263
360.0508
370.244
380.987
390.449
40.862
400.504
410.186
420.417
430.525
440.778
450.191
460.701
470.615
480.906
490.253
50.89
500.668
510.922
520.857
530.458
540.825
550.589
560.715
570.8
580.118
590.369
60.981
600.523
610.0755
620.204
630.825
640.917
650.678
660.332
670.986
680.928
690.377
70.559
700.116
710.122
720.445
730.74
740.949
750.0103
760.0065
770.00608
780.869
790.666
80.525
800.601
810.335
820.397
830.841
840.0552
850.864
860.0593
870.61
880.713
890.00336
90.594
900.891
910.287
920.878
930.712
940.302
950.11
960.63
970.508
980.242
991.49582e-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: CNhs12343


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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