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FF:12241-129G9: 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 17:21, 29 March 2012


Name:Basophils, 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 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-Peripheral0.144
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-0.197
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-Whole0.411
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-Whole0.252
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: CNhs12546

Jaspar motifP-value
MA0002.29.04749e-16
MA0003.10.0792
MA0004.10.659
MA0006.10.94
MA0007.10.68
MA0009.10.289
MA0014.10.623
MA0017.10.24
MA0018.26.63923e-5
MA0019.10.563
MA0024.10.0207
MA0025.16.65797e-5
MA0027.10.764
MA0028.10.94
MA0029.10.829
MA0030.10.0097
MA0031.10.0255
MA0035.20.536
MA0038.10.459
MA0039.20.491
MA0040.10.0345
MA0041.10.269
MA0042.10.246
MA0043.11.50596e-10
MA0046.10.138
MA0047.20.208
MA0048.10.617
MA0050.11.541e-5
MA0051.10.00687
MA0052.10.02
MA0055.10.549
MA0057.10.46
MA0058.10.393
MA0059.10.742
MA0060.10.0014
MA0061.11.21563e-15
MA0062.22.71372e-5
MA0065.20.0394
MA0066.10.0159
MA0067.17.3536e-7
MA0068.10.0833
MA0069.10.666
MA0070.10.0795
MA0071.10.249
MA0072.10.229
MA0073.10.153
MA0074.10.28
MA0076.10.785
MA0077.10.141
MA0078.10.571
MA0079.20.529
MA0080.22.93618e-14
MA0081.11.69924e-4
MA0083.10.631
MA0084.10.696
MA0087.10.875
MA0088.10.364
MA0090.10.0508
MA0091.10.856
MA0092.10.562
MA0093.10.717
MA0099.21.22572e-35
MA0100.10.938
MA0101.12.2788e-14
MA0102.24.65974e-8
MA0103.10.0715
MA0104.20.644
MA0105.14.08438e-16
MA0106.10.27
MA0107.11.58853e-17
MA0108.20.239
MA0111.10.894
MA0112.22.75002e-4
MA0113.10.767
MA0114.10.502
MA0115.10.333
MA0116.12.151e-4
MA0117.10.00893
MA0119.10.883
MA0122.10.693
MA0124.10.877
MA0125.10.186
MA0131.10.792
MA0135.10.125
MA0136.16.69435e-20
MA0137.20.193
MA0138.20.34
MA0139.10.827
MA0140.10.576
MA0141.10.256
MA0142.10.923
MA0143.10.707
MA0144.10.119
MA0145.10.272
MA0146.10.176
MA0147.10.83
MA0148.10.291
MA0149.10.402
MA0150.11.66485e-15
MA0152.10.101
MA0153.10.0985
MA0154.16.00636e-4
MA0155.10.803
MA0156.12.99455e-17
MA0157.10.112
MA0159.10.116
MA0160.10.0409
MA0162.10.74
MA0163.11.40831e-6
MA0164.10.99
MA0258.10.0141
MA0259.10.604



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: CNhs12546

Novel motifP-value
10.421
100.0782
1000.487
1010.979
1020.969
1030.36
1040.413
1050.0693
1069.56167e-4
1070.719
1080.598
1090.178
110.389
1100.364
1110.313
1120.397
1130.419
1140.132
1150.152
1160.517
1170.0534
1180.292
1190.775
120.222
1200.76
1210.354
1220.359
1230.591
1240.981
1250.601
1260.0931
1270.473
1280.0799
1290.964
130.227
1300.429
1310.9
1320.0376
1330.632
1340.997
1350.388
1360.962
1370.00337
1380.356
1390.134
140.345
1400.663
1410.551
1420.163
1430.00501
1440.698
1450.706
1460.988
1470.421
1480.127
1490.895
150.142
1500.543
1510.223
1520.157
1530.882
1540.893
1550.392
1560.621
1570.86
1580.0659
1590.0874
160.778
1600.872
1610.822
1620.174
1630.476
1640.187
1650.297
1660.575
1670.651
1680.171
1690.0268
170.395
180.276
190.623
20.729
200.47
210.886
220.236
230.0989
240.522
250.191
260.267
270.988
280.385
290.163
30.386
300.52
310.81
320.259
330.214
340.598
350.193
360.0926
370.137
380.566
390.969
40.923
400.119
410.00173
420.46
430.0531
440.641
450.668
460.364
470.775
480.707
490.144
50.196
500.81
510.429
520.435
530.506
540.498
550.885
560.838
570.676
580.115
590.195
60.982
600.0706
610.425
620.0731
630.946
640.476
650.322
660.226
670.732
680.602
690.727
70.202
700.14
710.0615
720.276
730.153
740.211
750.188
760.413
770.968
780.563
790.912
80.865
800.0137
810.533
820.445
830.0215
840.569
850.0506
860.0484
870.313
880.711
890.876
90.195
900.235
910.46
920.469
930.178
940.0901
950.0656
960.576
970.922
980.214
990.00317



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: CNhs12546


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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