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FF:12243-129H2: 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, donor3
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-Peripheral0.166
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-Basophils0.0625
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.179
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0625
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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-Whole0.35
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-Whole0.166
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: CNhs12575

Jaspar motifP-value
MA0002.21.04594e-13
MA0003.10.183
MA0004.10.376
MA0006.10.564
MA0007.10.644
MA0009.10.291
MA0014.10.809
MA0017.10.359
MA0018.21.29157e-4
MA0019.10.983
MA0024.10.0187
MA0025.11.49032e-5
MA0027.10.879
MA0028.10.0952
MA0029.10.39
MA0030.10.0469
MA0031.10.0698
MA0035.20.59
MA0038.10.814
MA0039.20.605
MA0040.10.143
MA0041.10.274
MA0042.10.249
MA0043.12.60682e-11
MA0046.10.0657
MA0047.20.355
MA0048.10.662
MA0050.18.27689e-6
MA0051.10.01
MA0052.11.31634e-4
MA0055.10.39
MA0057.10.236
MA0058.10.185
MA0059.10.741
MA0060.10.00113
MA0061.11.83643e-20
MA0062.20.00389
MA0065.20.0872
MA0066.10.019
MA0067.14.18416e-8
MA0068.10.0194
MA0069.10.654
MA0070.10.0376
MA0071.10.412
MA0072.10.399
MA0073.10.0523
MA0074.10.284
MA0076.10.265
MA0077.10.167
MA0078.10.679
MA0079.20.829
MA0080.29.28751e-15
MA0081.11.35983e-4
MA0083.10.793
MA0084.10.827
MA0087.10.891
MA0088.10.0548
MA0090.10.109
MA0091.10.996
MA0092.10.48
MA0093.10.453
MA0099.25.15742e-45
MA0100.10.621
MA0101.18.41152e-18
MA0102.22.17319e-10
MA0103.10.0397
MA0104.20.521
MA0105.11.14433e-16
MA0106.10.129
MA0107.17.23613e-22
MA0108.20.804
MA0111.10.953
MA0112.20.00257
MA0113.10.602
MA0114.10.807
MA0115.10.0992
MA0116.10.0028
MA0117.10.00985
MA0119.10.946
MA0122.10.939
MA0124.10.721
MA0125.10.199
MA0131.10.679
MA0135.10.334
MA0136.14.37326e-18
MA0137.20.722
MA0138.20.241
MA0139.10.304
MA0140.10.346
MA0141.10.395
MA0142.10.973
MA0143.10.714
MA0144.10.209
MA0145.10.416
MA0146.10.252
MA0147.10.789
MA0148.10.437
MA0149.10.882
MA0150.13.01374e-18
MA0152.10.134
MA0153.10.00584
MA0154.16.25726e-4
MA0155.10.683
MA0156.18.50767e-15
MA0157.10.0966
MA0159.10.231
MA0160.10.0552
MA0162.10.861
MA0163.14.90465e-4
MA0164.10.863
MA0258.10.0788
MA0259.10.678



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: CNhs12575

Novel motifP-value
10.564
100.0699
1000.432
1010.87
1020.926
1030.588
1040.431
1050.0332
1062.34147e-4
1070.434
1080.672
1090.4
110.534
1100.551
1110.287
1120.592
1130.0907
1140.23
1150.149
1160.49
1170.101
1180.324
1190.949
120.171
1200.564
1210.263
1220.217
1230.262
1240.863
1250.605
1260.191
1270.417
1280.0518
1290.76
130.254
1300.414
1310.719
1320.0116
1330.38
1340.863
1350.4
1360.9
1370.0031
1380.288
1390.153
140.318
1400.235
1410.771
1420.118
1430.00639
1440.773
1450.76
1460.839
1470.291
1480.0734
1490.69
150.214
1500.585
1510.143
1520.0721
1530.652
1540.476
1550.455
1560.698
1570.857
1580.0602
1590.129
160.844
1600.921
1610.942
1620.0708
1630.327
1640.216
1650.289
1660.592
1670.61
1680.142
1690.0449
170.405
180.281
190.874
20.681
200.519
210.828
220.247
230.142
240.597
250.266
260.219
270.794
280.523
290.207
30.415
300.524
310.776
320.172
330.452
340.563
350.297
360.177
370.237
380.69
390.995
40.886
400.219
410.00179
420.522
430.0382
440.559
450.642
460.431
470.849
480.945
490.134
50.245
500.847
510.422
520.408
530.418
540.46
550.663
560.963
570.736
580.205
590.269
60.797
600.0833
610.484
620.131
630.937
640.596
650.433
660.138
670.626
680.248
690.471
70.232
700.205
710.098
720.259
730.151
740.28
750.286
760.412
770.963
780.638
790.643
80.727
800.013
810.599
820.55
830.102
840.455
850.0526
860.0435
870.298
880.726
890.999
90.265
900.421
910.303
920.546
930.293
940.095
950.281
960.737
970.849
980.332
999.363e-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: CNhs12575


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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