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FF:11233-116C9: 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 16:35, 29 March 2012


Name:Neutrophils, 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 stage66 years old adult
sexmale
age66
cell typeneutrophil
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNeu734
catalog number3H100-94-25
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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: CNhs10862

Jaspar motifP-value
MA0002.23.55745e-9
MA0003.10.25
MA0004.10.704
MA0006.10.409
MA0007.10.689
MA0009.10.0286
MA0014.10.544
MA0017.10.112
MA0018.20.00755
MA0019.10.208
MA0024.10.00242
MA0025.10.0264
MA0027.10.899
MA0028.10.335
MA0029.10.409
MA0030.19.41645e-4
MA0031.10.00293
MA0035.20.93
MA0038.10.0124
MA0039.20.475
MA0040.10.0176
MA0041.10.846
MA0042.10.396
MA0043.11.42884e-8
MA0046.10.0681
MA0047.20.107
MA0048.10.936
MA0050.13.87749e-4
MA0051.10.145
MA0052.10.0048
MA0055.10.16
MA0057.10.342
MA0058.10.747
MA0059.10.792
MA0060.18.82433e-8
MA0061.18.07122e-8
MA0062.20.14
MA0065.20.0285
MA0066.10.089
MA0067.10.0114
MA0068.10.243
MA0069.10.852
MA0070.10.00767
MA0071.10.184
MA0072.10.546
MA0073.10.379
MA0074.10.336
MA0076.10.462
MA0077.10.309
MA0078.10.743
MA0079.20.543
MA0080.21.82396e-16
MA0081.14.63101e-5
MA0083.10.523
MA0084.10.661
MA0087.10.895
MA0088.10.349
MA0090.10.0868
MA0091.10.868
MA0092.10.798
MA0093.10.546
MA0099.21.19574e-4
MA0100.10.824
MA0101.11.6844e-7
MA0102.29.69429e-10
MA0103.10.505
MA0104.20.382
MA0105.12.85049e-10
MA0106.10.311
MA0107.12.88903e-9
MA0108.26.99574e-6
MA0111.10.395
MA0112.20.00133
MA0113.10.458
MA0114.10.338
MA0115.10.884
MA0116.17.94889e-4
MA0117.10.197
MA0119.10.34
MA0122.10.714
MA0124.10.74
MA0125.10.163
MA0131.10.792
MA0135.10.525
MA0136.19.72608e-18
MA0137.20.34
MA0138.20.789
MA0139.10.733
MA0140.10.613
MA0141.10.0942
MA0142.10.483
MA0143.10.62
MA0144.10.131
MA0145.10.176
MA0146.10.0867
MA0147.10.319
MA0148.10.344
MA0149.10.603
MA0150.11.08249e-8
MA0152.10.155
MA0153.10.0839
MA0154.10.00142
MA0155.10.524
MA0156.11.2962e-8
MA0157.10.0085
MA0159.10.0397
MA0160.10.0362
MA0162.10.684
MA0163.11.01242e-4
MA0164.10.926
MA0258.10.00919
MA0259.10.274



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: CNhs10862

Novel motifP-value
10.0756
100.0315
1000.641
1010.396
1020.952
1030.328
1040.745
1050.354
1066.30979e-4
1070.276
1080.709
1090.201
110.136
1100.366
1110.122
1120.288
1130.509
1140.0144
1150.706
1160.949
1170.0144
1180.0587
1190.179
120.624
1200.818
1210.59
1220.815
1230.0144
1240.624
1250.0668
1260.202
1270.587
1280.00845
1290.606
130.344
1300.644
1310.611
1320.113
1330.644
1340.54
1350.233
1360.493
1370.0014
1380.0949
1390.0789
140.245
1400.191
1410.321
1420.659
1430.0319
1440.75
1450.672
1460.355
1470.536
1480.0754
1490.219
150.0418
1500.603
1510.287
1520.216
1530.394
1540.8
1550.0716
1560.633
1570.909
1580.00589
1590.747
160.351
1600.785
1610.82
1620.544
1630.504
1640.0976
1650.184
1660.725
1670.587
1680.518
1690.0344
170.185
180.0871
190.23
20.68
200.604
210.668
220.244
230.00792
240.459
250.314
260.0795
270.62
280.357
290.368
30.109
300.619
310.737
320.742
330.337
340.656
350.0697
360.18
370.12
380.365
390.988
40.616
400.422
410.0217
420.358
430.066
440.616
450.595
460.172
470.384
480.506
490.0826
50.0987
500.859
510.367
520.202
530.238
540.281
550.339
560.475
570.917
580.154
590.0824
60.634
600.0203
610.257
620.0366
630.36
640.405
650.205
660.216
670.388
680.387
690.98
70.26
700.0711
710.0336
720.568
730.309
740.159
750.148
760.237
770.481
780.236
790.197
80.816
800.128
810.289
820.0344
830.781
840.652
850.0536
860.0373
870.827
880.643
890.122
90.27
900.0843
910.186
920.159
930.291
940.0276
950.635
960.343
970.926
980.134
990.0671



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: CNhs10862


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)
0000775 (neutrophil)
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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