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FF:10830-111D2: 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:FKH-1
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
sexmale
age60
cell typemyeloid progenitor cell
cell lineFKH-1
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-penis0.824
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-lymphoma0.439
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs13503

Jaspar motifP-value
MA0002.20.0455
MA0003.10.907
MA0004.10.0283
MA0006.10.228
MA0007.10.727
MA0009.10.289
MA0014.10.222
MA0017.10.393
MA0018.21.11661e-4
MA0019.10.00617
MA0024.13.39036e-4
MA0025.10.666
MA0027.10.0462
MA0028.10.0124
MA0029.10.834
MA0030.10.107
MA0031.10.0602
MA0035.20.00461
MA0038.10.00303
MA0039.20.0732
MA0040.10.466
MA0041.10.385
MA0042.10.471
MA0043.10.0704
MA0046.10.495
MA0047.20.39
MA0048.10.14
MA0050.13.79535e-4
MA0051.10.0469
MA0052.10.0361
MA0055.10.368
MA0057.10.658
MA0058.10.0397
MA0059.10.00378
MA0060.10.761
MA0061.10.475
MA0062.27.97342e-6
MA0065.20.147
MA0066.10.794
MA0067.10.348
MA0068.10.126
MA0069.10.941
MA0070.10.321
MA0071.10.155
MA0072.10.482
MA0073.10.869
MA0074.10.685
MA0076.10.0564
MA0077.10.449
MA0078.10.689
MA0079.20.136
MA0080.23.33883e-11
MA0081.10.0296
MA0083.10.0063
MA0084.10.753
MA0087.10.447
MA0088.10.0766
MA0090.10.00393
MA0091.10.509
MA0092.10.891
MA0093.10.042
MA0099.22.92879e-4
MA0100.10.0407
MA0101.10.809
MA0102.20.117
MA0103.10.369
MA0104.23.03059e-4
MA0105.10.00737
MA0106.10.312
MA0107.10.162
MA0108.22.74526e-6
MA0111.10.289
MA0112.20.378
MA0113.10.946
MA0114.10.333
MA0115.10.517
MA0116.10.00293
MA0117.10.997
MA0119.10.448
MA0122.10.888
MA0124.10.813
MA0125.10.824
MA0131.10.0913
MA0135.10.917
MA0136.13.11863e-14
MA0137.20.414
MA0138.20.904
MA0139.10.965
MA0140.10.00372
MA0141.10.129
MA0142.10.491
MA0143.10.929
MA0144.10.64
MA0145.10.169
MA0146.10.56
MA0147.11.01031e-4
MA0148.10.242
MA0149.10.0614
MA0150.10.432
MA0152.10.0799
MA0153.10.14
MA0154.10.15
MA0155.10.765
MA0156.11.34009e-7
MA0157.10.668
MA0159.10.601
MA0160.10.0502
MA0162.10.599
MA0163.11.88784e-6
MA0164.10.653
MA0258.10.027
MA0259.10.0858



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: CNhs13503

Novel motifP-value
10.134
100.0152
1000.956
1010.0888
1020.953
1030.644
1040.696
1050.807
1060.831
1070.54
1080.291
1090.41
110.0781
1100.442
1110.00639
1120.483
1130.241
1140.105
1150.0855
1160.35
1170.177
1180.0965
1190.0755
120.77
1200.631
1210.477
1220.794
1233.93463e-4
1240.115
1250.0365
1260.467
1270.144
1280.612
1290.201
130.0302
1300.893
1310.219
1320.793
1330.8
1340.26
1350.728
1360.422
1370.552
1380.106
1390.0953
140.719
1400.0173
1410.864
1420.156
1430.539
1440.942
1450.159
1460.961
1470.475
1480.739
1490.501
150.375
1500.884
1510.396
1520.0486
1530.68
1540.902
1550.0766
1560.803
1570.89
1580.0322
1590.0186
160.522
1600.473
1610.214
1620.251
1630.499
1640.17
1650.697
1660.663
1670.141
1680.623
1690.29
170.64
180.458
190.775
20.674
200.544
210.479
220.917
230.189
240.808
250.517
260.012
270.903
280.718
290.375
30.0477
300.0991
310.938
320.0337
330.583
340.813
350.0358
360.0304
370.321
380.61
390.914
40.0265
400.545
410.9
420.0809
430.563
440.233
450.896
460.0367
470.176
480.13
490.038
50.441
500.884
510.494
520.863
530.0764
540.765
550.758
560.768
570.124
580.298
590.849
60.802
600.431
610.0419
620.223
630.438
640.295
650.657
660.171
670.895
680.737
690.868
70.0533
700.988
710.0921
720.339
730.415
740.644
750.0655
760.0435
770.473
780.116
790.32
80.214
800.485
810.49
820.45
830.504
840.966
850.541
860.749
870.272
880.338
890.645
90.993
900.148
910.448
920.343
930.365
940.249
950.736
960.238
970.678
980.108
990.568



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: CNhs13503


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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