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FF:12245-129H4: 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:Eosinophils, 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 typeeosinophil
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number3H100-90-5
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
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
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
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
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: CNhs12548

Jaspar motifP-value
MA0002.23.52665e-12
MA0003.10.191
MA0004.10.858
MA0006.10.53
MA0007.10.454
MA0009.10.0783
MA0014.10.954
MA0017.10.0863
MA0018.22.90801e-7
MA0019.10.915
MA0024.10.00351
MA0025.15.62352e-7
MA0027.10.79
MA0028.10.928
MA0029.10.822
MA0030.11.41453e-5
MA0031.17.10233e-4
MA0035.20.919
MA0038.10.2
MA0039.20.781
MA0040.10.00296
MA0041.10.258
MA0042.10.0369
MA0043.11.17357e-15
MA0046.10.136
MA0047.20.0355
MA0048.10.706
MA0050.14.0852e-4
MA0051.10.08
MA0052.10.797
MA0055.10.233
MA0057.10.225
MA0058.10.599
MA0059.10.915
MA0060.12.08368e-4
MA0061.11.25687e-16
MA0062.23.49697e-5
MA0065.20.0384
MA0066.10.0387
MA0067.12.86593e-5
MA0068.10.468
MA0069.10.322
MA0070.10.0515
MA0071.10.13
MA0072.10.682
MA0073.10.122
MA0074.10.27
MA0076.10.524
MA0077.10.375
MA0078.10.454
MA0079.20.866
MA0080.21.62291e-15
MA0081.12.62295e-5
MA0083.10.0546
MA0084.10.491
MA0087.10.601
MA0088.10.162
MA0090.10.131
MA0091.10.94
MA0092.10.901
MA0093.10.916
MA0099.23.35817e-16
MA0100.10.941
MA0101.15.39674e-18
MA0102.21.95285e-13
MA0103.10.793
MA0104.20.655
MA0105.12.94427e-14
MA0106.10.218
MA0107.15.64406e-24
MA0108.20.0765
MA0111.10.828
MA0112.20.00459
MA0113.10.722
MA0114.10.427
MA0115.10.738
MA0116.10.00293
MA0117.10.0141
MA0119.10.89
MA0122.10.391
MA0124.10.764
MA0125.10.169
MA0131.10.82
MA0135.10.0504
MA0136.14.61315e-20
MA0137.20.049
MA0138.20.212
MA0139.10.976
MA0140.10.629
MA0141.10.0455
MA0142.10.676
MA0143.10.867
MA0144.10.0481
MA0145.10.224
MA0146.10.156
MA0147.10.51
MA0148.10.156
MA0149.10.84
MA0150.14.34929e-14
MA0152.10.0885
MA0153.10.11
MA0154.16.40618e-4
MA0155.10.426
MA0156.11.35154e-14
MA0157.10.0246
MA0159.10.0253
MA0160.10.00713
MA0162.10.924
MA0163.10.00355
MA0164.10.936
MA0258.10.0617
MA0259.10.318



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: CNhs12548

Novel motifP-value
10.245
100.0925
1000.476
1010.86
1020.945
1030.286
1040.533
1050.252
1064.6952e-4
1070.748
1080.43
1090.203
110.262
1100.596
1110.383
1120.393
1130.515
1140.0523
1150.375
1160.633
1170.0208
1180.112
1190.443
120.264
1200.568
1210.836
1220.493
1230.464
1240.867
1250.166
1260.0926
1270.458
1280.0309
1290.619
130.286
1300.889
1310.575
1320.0785
1330.949
1340.583
1350.199
1360.697
1377.04679e-4
1380.181
1390.0955
140.347
1400.639
1410.286
1420.594
1430.0185
1440.95
1450.779
1460.413
1470.656
1480.169
1490.643
150.123
1500.732
1510.254
1520.146
1530.781
1541
1550.145
1560.899
1570.976
1580.00467
1590.412
160.582
1600.926
1610.734
1620.0582
1630.351
1640.212
1650.301
1660.722
1670.817
1680.182
1690.0863
170.303
180.174
190.541
20.93
200.539
210.964
220.162
230.0206
240.379
250.314
260.156
270.894
280.351
290.386
30.324
300.666
310.897
320.307
330.333
340.569
350.139
360.228
370.103
380.513
390.795
40.824
400.311
410.00333
420.581
430.0625
440.93
450.42
460.386
470.641
480.734
490.133
50.142
500.956
510.398
520.298
530.389
540.345
550.949
560.792
570.532
580.223
590.0816
60.842
600.0408
610.299
620.0934
630.677
640.599
650.233
660.291
670.491
680.339
690.519
70.26
700.22
710.0425
720.452
730.191
740.0944
750.256
760.191
770.665
780.245
790.922
80.653
800.0284
810.428
820.106
830.132
840.439
850.0746
860.021
870.319
880.696
890.127
90.218
900.316
910.486
920.398
930.064
940.0661
950.208
960.503
970.928
980.122
990.0134



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: CNhs12548


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)
0000771 (eosinophil)
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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