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FF:12242-129H1: 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 17:22, 29 March 2012


Name:Basophils, 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 typebasophil
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number3H100-93-5
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-Peripheral0.141
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-Basophils0.141
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.188
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.247
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-Whole0.61
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: CNhs12563

Jaspar motifP-value
MA0002.21.38821e-14
MA0003.10.944
MA0004.10.649
MA0006.10.498
MA0007.10.342
MA0009.10.136
MA0014.10.989
MA0017.10.493
MA0018.20.00122
MA0019.10.987
MA0024.10.0799
MA0025.11.62626e-4
MA0027.10.869
MA0028.10.698
MA0029.10.418
MA0030.10.034
MA0031.10.0132
MA0035.20.862
MA0038.10.557
MA0039.20.777
MA0040.10.188
MA0041.10.746
MA0042.10.648
MA0043.15.75609e-8
MA0046.10.138
MA0047.20.332
MA0048.10.572
MA0050.11.02412e-6
MA0051.10.0117
MA0052.10.271
MA0055.10.188
MA0057.10.253
MA0058.10.438
MA0059.10.64
MA0060.15.64288e-4
MA0061.19.87117e-17
MA0062.21.22739e-6
MA0065.20.196
MA0066.10.0293
MA0067.16.92611e-6
MA0068.10.0922
MA0069.10.525
MA0070.10.0491
MA0071.10.46
MA0072.10.334
MA0073.10.427
MA0074.10.402
MA0076.10.439
MA0077.10.174
MA0078.10.675
MA0079.20.382
MA0080.22.18717e-14
MA0081.11.5226e-4
MA0083.10.527
MA0084.10.353
MA0087.10.836
MA0088.10.415
MA0090.10.0258
MA0091.10.922
MA0092.10.612
MA0093.10.719
MA0099.26.13769e-31
MA0100.10.708
MA0101.16.31085e-12
MA0102.24.12771e-7
MA0103.10.0689
MA0104.20.367
MA0105.11.46812e-17
MA0106.10.207
MA0107.12.43293e-14
MA0108.20.0235
MA0111.10.524
MA0112.20.0258
MA0113.10.813
MA0114.10.736
MA0115.10.18
MA0116.12.34314e-4
MA0117.10.0111
MA0119.10.707
MA0122.10.884
MA0124.10.873
MA0125.10.103
MA0131.10.932
MA0135.10.814
MA0136.11.99387e-20
MA0137.20.771
MA0138.20.166
MA0139.10.943
MA0140.10.841
MA0141.10.635
MA0142.10.888
MA0143.10.819
MA0144.10.326
MA0145.10.659
MA0146.10.786
MA0147.10.481
MA0148.10.245
MA0149.10.562
MA0150.11.26398e-13
MA0152.10.145
MA0153.10.0379
MA0154.10.00331
MA0155.10.605
MA0156.19.32154e-19
MA0157.10.0271
MA0159.10.187
MA0160.10.148
MA0162.10.642
MA0163.12.2898e-5
MA0164.11
MA0258.10.0849
MA0259.10.971



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: CNhs12563

Novel motifP-value
10.346
100.0191
1000.495
1010.603
1020.824
1030.342
1040.421
1050.141
1060.0101
1070.962
1080.522
1090.352
110.345
1100.605
1110.265
1120.525
1130.124
1140.117
1150.16
1160.461
1170.0264
1180.32
1190.861
120.276
1200.943
1210.564
1220.48
1230.0977
1240.508
1250.541
1260.135
1270.627
1280.189
1290.998
130.293
1300.381
1310.855
1320.0317
1330.358
1340.976
1350.337
1360.681
1379.61216e-4
1380.316
1390.0534
140.3
1400.497
1410.466
1420.123
1430.00149
1440.683
1450.546
1460.854
1470.231
1480.111
1490.764
150.139
1500.652
1510.147
1520.932
1530.688
1540.4
1550.379
1560.536
1570.657
1580.0786
1590.0321
160.909
1600.717
1610.873
1620.0695
1630.509
1640.175
1650.32
1660.797
1670.337
1680.175
1690.466
170.602
180.271
190.931
20.574
200.484
210.899
220.674
230.22
240.547
250.142
260.3
270.946
280.328
290.127
30.268
300.305
310.884
320.0726
330.424
340.825
350.12
360.0825
370.217
380.696
390.847
40.92
400.466
410.00334
420.283
430.0565
440.653
450.997
460.349
470.722
480.674
490.112
50.188
500.663
510.458
520.621
530.369
540.55
550.8
560.918
570.951
580.0955
590.725
60.936
600.119
610.332
620.0664
630.959
640.512
650.556
660.263
670.877
680.344
690.707
70.194
700.15
710.0466
720.302
730.378
740.137
750.0761
760.15
770.52
780.661
790.781
80.927
800.00511
810.43
820.373
830.0411
840.498
850.0837
860.0226
870.511
880.811
890.587
90.402
900.0759
910.483
920.381
930.177
940.0796
950.132
960.387
970.96
980.389
993.68457e-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: CNhs12563


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)
0000049 (common myeloid progenitor)
0000081 (blood cell)
0000094 (granulocyte)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000767 (basophil)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
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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