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FF:10831-111D3: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101035
|fonse_cell_line=FF:0101035
|fonse_cell_line_closure=FF:0101035
|fonse_cell_line_closure=FF:0101035

Revision as of 17:35, 29 March 2012


Name:acute myeloid leukemia (FAB M4) cell line:HNT-34
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
sexfemale
age45
cell typemyeloid progenitor cell
cell lineHNT-34
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.292
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.532
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13504

Jaspar motifP-value
MA0002.20.0669
MA0003.10.998
MA0004.10.339
MA0006.10.365
MA0007.10.936
MA0009.10.0518
MA0014.10.343
MA0017.10.0451
MA0018.29.05474e-5
MA0019.10.0596
MA0024.11.83709e-7
MA0025.10.0169
MA0027.10.0743
MA0028.10.00999
MA0029.10.742
MA0030.10.0115
MA0031.10.598
MA0035.20.00428
MA0038.16.01317e-4
MA0039.20.103
MA0040.10.635
MA0041.10.0958
MA0042.10.197
MA0043.10.00302
MA0046.10.107
MA0047.20.54
MA0048.10.226
MA0050.10.956
MA0051.10.265
MA0052.10.00671
MA0055.10.0986
MA0057.10.669
MA0058.10.287
MA0059.10.0106
MA0060.10.0791
MA0061.10.595
MA0062.21.59708e-5
MA0065.20.00348
MA0066.10.405
MA0067.10.258
MA0068.10.395
MA0069.10.193
MA0070.10.979
MA0071.10.118
MA0072.10.217
MA0073.10.696
MA0074.10.656
MA0076.10.0131
MA0077.10.655
MA0078.10.573
MA0079.20.233
MA0080.24.00589e-9
MA0081.10.00212
MA0083.12.46969e-5
MA0084.10.829
MA0087.10.446
MA0088.10.00585
MA0090.10.00113
MA0091.10.884
MA0092.10.909
MA0093.10.336
MA0099.21.08416e-8
MA0100.10.0551
MA0101.10.502
MA0102.21
MA0103.10.236
MA0104.20.00389
MA0105.13.27321e-4
MA0106.10.175
MA0107.10.0589
MA0108.27.00771e-11
MA0111.10.224
MA0112.20.114
MA0113.10.85
MA0114.10.11
MA0115.10.169
MA0116.12.86937e-5
MA0117.10.54
MA0119.10.482
MA0122.10.948
MA0124.10.879
MA0125.10.615
MA0131.10.418
MA0135.10.783
MA0136.11.25485e-10
MA0137.20.0236
MA0138.20.482
MA0139.10.114
MA0140.13.5509e-4
MA0141.10.125
MA0142.10.236
MA0143.10.812
MA0144.10.195
MA0145.10.226
MA0146.10.185
MA0147.16.10664e-4
MA0148.10.497
MA0149.10.0997
MA0150.10.0441
MA0152.10.264
MA0153.19.90581e-4
MA0154.10.0226
MA0155.10.976
MA0156.14.04956e-7
MA0157.10.724
MA0159.10.53
MA0160.10.144
MA0162.10.72
MA0163.16.26761e-13
MA0164.10.665
MA0258.10.096
MA0259.10.166



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: CNhs13504

Novel motifP-value
10.073
100.046
1000.789
1010.276
1020.488
1030.0723
1040.639
1050.825
1060.963
1070.777
1080.841
1090.133
110.0846
1100.198
1110.0485
1120.861
1130.76
1140.029
1150.447
1160.266
1170.0441
1180.0488
1190.693
120.66
1200.253
1210.259
1220.954
1230.00826
1240.0046
1250.0888
1260.218
1270.136
1280.947
1290.0577
130.0114
1300.683
1310.384
1320.883
1330.878
1340.577
1350.621
1360.146
1370.636
1380.3
1390.496
140.801
1400.191
1410.124
1420.414
1430.305
1440.564
1450.119
1460.917
1470.0536
1480.224
1490.816
150.28
1500.788
1510.8
1520.25
1530.8
1540.897
1550.0951
1560.72
1570.216
1580.707
1590.698
160.455
1600.049
1610.00837
1620.584
1630.986
1640.335
1650.448
1660.705
1670.0827
1680.873
1690.409
170.824
180.733
190.811
20.76
200.761
210.23
220.743
230.0251
240.104
250.288
260.0584
270.537
280.84
290.0532
30.0878
300.333
310.672
320.0787
330.182
340.862
350.154
360.0515
370.17
380.499
390.562
40.172
400.291
410.822
420.129
430.484
440.12
450.801
460.072
470.0449
480.0541
490.183
50.863
500.815
510.687
520.379
530.523
540.751
550.323
560.525
570.0562
580.193
590.381
60.582
600.962
610.11
620.129
630.595
640.232
650.544
660.0826
670.897
680.837
690.494
70.0318
700.304
710.0147
720.893
730.773
740.987
750.032
760.426
770.972
780.00476
790.0656
80.0354
800.185
810.419
820.601
830.784
840.689
850.421
860.748
870.779
880.285
890.841
90.912
900.0456
910.74
920.888
930.968
940.961
950.0819
960.838
970.336
980.159
990.772



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: CNhs13504


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060083 (immune system cancer)
1240 (leukemia)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)
8692 (myeloid leukemia)

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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