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FF:11314-117C9: 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 17:03, 29 March 2012


Name:Neutrophils, 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 stage38 years old adult
sexmale
age38
cell typeneutrophil
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNeu735
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
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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: CNhs11959

Jaspar motifP-value
MA0002.22.17036e-6
MA0003.10.347
MA0004.10.645
MA0006.10.391
MA0007.10.955
MA0009.10.00714
MA0014.10.255
MA0017.10.112
MA0018.20.77
MA0019.10.088
MA0024.10.00329
MA0025.10.396
MA0027.10.932
MA0028.10.0457
MA0029.10.202
MA0030.10.215
MA0031.10.281
MA0035.20.81
MA0038.10.00122
MA0039.20.107
MA0040.10.337
MA0041.10.279
MA0042.10.948
MA0043.10.019
MA0046.10.0235
MA0047.20.366
MA0048.10.97
MA0050.10.182
MA0051.10.73
MA0052.10.00611
MA0055.10.125
MA0057.10.495
MA0058.10.54
MA0059.10.926
MA0060.18.11451e-10
MA0061.14.91857e-4
MA0062.20.212
MA0065.20.0168
MA0066.10.0974
MA0067.10.299
MA0068.10.117
MA0069.10.956
MA0070.10.00531
MA0071.10.181
MA0072.10.309
MA0073.10.525
MA0074.10.226
MA0076.10.03
MA0077.10.286
MA0078.10.787
MA0079.20.313
MA0080.21.24739e-14
MA0081.10.00236
MA0083.10.952
MA0084.10.714
MA0087.10.605
MA0088.10.443
MA0090.10.264
MA0091.10.414
MA0092.10.646
MA0093.10.451
MA0099.20.287
MA0100.10.624
MA0101.10.00782
MA0102.25.11095e-4
MA0103.10.198
MA0104.20.421
MA0105.13.39616e-9
MA0106.10.796
MA0107.10.00282
MA0108.27.83385e-7
MA0111.10.387
MA0112.21.57734e-4
MA0113.10.572
MA0114.10.282
MA0115.10.892
MA0116.12.75194e-4
MA0117.10.639
MA0119.10.156
MA0122.10.875
MA0124.10.505
MA0125.10.0756
MA0131.10.527
MA0135.10.544
MA0136.11.06606e-10
MA0137.20.375
MA0138.20.523
MA0139.10.762
MA0140.10.937
MA0141.10.107
MA0142.10.822
MA0143.10.34
MA0144.10.525
MA0145.10.189
MA0146.10.196
MA0147.10.445
MA0148.10.753
MA0149.10.44
MA0150.13.20077e-4
MA0152.10.167
MA0153.10.0368
MA0154.10.0021
MA0155.10.568
MA0156.10.0126
MA0157.10.103
MA0159.10.0337
MA0160.10.107
MA0162.10.473
MA0163.11.90574e-6
MA0164.10.857
MA0258.10.00196
MA0259.10.302



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: CNhs11959

Novel motifP-value
10.0546
100.0256
1000.85
1010.257
1020.979
1030.213
1040.687
1050.452
1063.8565e-4
1070.0644
1080.974
1090.263
110.071
1100.363
1110.0497
1120.172
1130.445
1140.0105
1150.931
1160.681
1170.0326
1180.11
1190.0571
120.895
1200.81
1210.269
1220.512
1230.00154
1240.438
1250.0715
1260.403
1270.793
1280.00193
1290.309
130.499
1300.247
1310.914
1320.532
1330.604
1340.53
1350.218
1360.428
1370.0122
1380.0775
1390.0295
140.35
1400.113
1410.277
1420.674
1430.0295
1440.794
1450.32
1460.438
1470.996
1480.0514
1490.148
150.0572
1500.495
1510.243
1520.283
1530.387
1540.614
1550.112
1560.975
1570.974
1580.0418
1590.725
160.272
1600.369
1610.623
1620.922
1630.466
1640.122
1650.229
1660.537
1670.146
1680.861
1690.0266
170.178
180.0809
190.194
20.638
200.794
210.42
220.33
230.0116
240.548
250.458
260.0712
270.416
280.461
290.396
30.0991
300.639
310.582
320.318
330.431
340.661
350.0575
360.258
370.159
380.268
390.733
40.633
400.592
410.107
420.368
430.0822
440.365
450.653
460.093
470.256
480.333
490.0822
50.148
500.884
510.318
520.137
530.246
540.286
550.323
560.426
570.544
580.151
590.0945
60.547
600.0174
610.433
620.0305
630.271
640.36
650.148
660.249
670.312
680.878
690.581
70.318
700.0252
710.0478
720.63
730.384
740.581
750.168
760.355
770.305
780.22
790.302
80.319
800.441
810.259
820.0267
830.99
840.558
850.0184
860.0689
870.913
880.735
890.133
90.325
900.0688
910.118
920.0666
930.674
940.0192
950.728
960.123
970.76
980.0889
990.427



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: CNhs11959


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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