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FF:12246-129H5: 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, 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 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
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C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
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: CNhs12549

Jaspar motifP-value
MA0002.27.64165e-12
MA0003.10.125
MA0004.10.931
MA0006.10.507
MA0007.10.896
MA0009.10.0709
MA0014.10.78
MA0017.10.0892
MA0018.21.36222e-4
MA0019.10.624
MA0024.10.00673
MA0025.18.19943e-6
MA0027.10.836
MA0028.10.193
MA0029.10.873
MA0030.11.32762e-4
MA0031.10.00387
MA0035.20.967
MA0038.10.133
MA0039.20.947
MA0040.10.00164
MA0041.10.132
MA0042.10.0209
MA0043.12.42591e-13
MA0046.10.31
MA0047.20.018
MA0048.10.656
MA0050.10.00124
MA0051.10.132
MA0052.10.769
MA0055.10.328
MA0057.10.231
MA0058.10.767
MA0059.10.739
MA0060.12.13981e-5
MA0061.11.16745e-14
MA0062.20.108
MA0065.20.0135
MA0066.10.00603
MA0067.13.18318e-4
MA0068.10.352
MA0069.10.33
MA0070.10.0173
MA0071.10.264
MA0072.10.793
MA0073.10.151
MA0074.10.189
MA0076.10.279
MA0077.10.303
MA0078.10.46
MA0079.20.666
MA0080.22.19194e-15
MA0081.16.25985e-5
MA0083.10.1
MA0084.10.929
MA0087.10.618
MA0088.10.259
MA0090.10.349
MA0091.10.937
MA0092.10.682
MA0093.10.975
MA0099.25.91061e-15
MA0100.10.949
MA0101.16.90177e-15
MA0102.29.89264e-12
MA0103.10.934
MA0104.20.823
MA0105.12.43383e-15
MA0106.10.483
MA0107.13.8186e-19
MA0108.20.226
MA0111.10.726
MA0112.29.82225e-4
MA0113.10.793
MA0114.10.278
MA0115.10.443
MA0116.17.08686e-4
MA0117.10.0329
MA0119.10.545
MA0122.10.515
MA0124.10.809
MA0125.10.202
MA0131.10.619
MA0135.10.131
MA0136.12.59506e-17
MA0137.20.0689
MA0138.20.744
MA0139.10.905
MA0140.10.567
MA0141.10.0639
MA0142.10.858
MA0143.10.771
MA0144.10.0375
MA0145.10.239
MA0146.10.14
MA0147.10.655
MA0148.10.114
MA0149.10.641
MA0150.15.76977e-13
MA0152.10.231
MA0153.10.124
MA0154.12.46299e-4
MA0155.10.496
MA0156.11.04935e-10
MA0157.10.0261
MA0159.10.0247
MA0160.10.0311
MA0162.10.594
MA0163.17.19641e-4
MA0164.10.899
MA0258.10.0187
MA0259.10.418



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: CNhs12549

Novel motifP-value
10.162
100.0786
1000.569
1010.743
1020.918
1030.269
1040.563
1050.134
1064.64773e-4
1070.324
1080.583
1090.193
110.228
1100.432
1110.378
1120.306
1130.417
1140.0239
1150.199
1160.917
1170.0617
1180.0966
1190.291
120.423
1200.606
1210.996
1220.666
1230.374
1240.69
1250.183
1260.123
1270.497
1280.0188
1290.517
130.441
1300.685
1310.667
1320.0999
1330.755
1340.485
1350.187
1360.72
1370.00105
1380.239
1390.11
140.309
1400.908
1410.504
1420.518
1430.00668
1440.964
1450.796
1460.679
1470.535
1480.121
1490.531
150.0762
1500.678
1510.268
1520.281
1530.884
1540.906
1550.277
1560.838
1570.961
1580.0124
1590.303
160.47
1600.769
1610.778
1620.0912
1630.413
1640.171
1650.232
1660.842
1670.998
1680.26
1690.0483
170.2
180.122
190.46
20.766
200.606
210.929
220.224
230.00747
240.525
250.325
260.141
270.798
280.339
290.405
30.333
300.768
310.751
320.72
330.39
340.536
350.134
360.157
370.133
380.402
390.885
40.724
400.237
410.00493
420.632
430.0648
440.95
450.403
460.304
470.625
480.634
490.104
50.115
500.877
510.348
520.229
530.301
540.288
550.861
560.609
570.791
580.195
590.0629
60.729
600.0289
610.307
620.0709
630.485
640.491
650.152
660.322
670.574
680.463
690.589
70.218
700.172
710.0587
720.548
730.35
740.0561
750.294
760.218
770.489
780.286
790.993
80.976
800.0268
810.415
820.073
830.0525
840.587
850.0654
860.0358
870.432
880.614
890.148
90.221
900.111
910.445
920.312
930.0778
940.0392
950.378
960.344
970.902
980.124
990.0342



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: CNhs12549


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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