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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000566,CL:0000723,CL:0000763,CL:0000837,CL:0000988,CL:0002032,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000566,CL:0000723,CL:0000763,CL:0000837,CL:0000988,CL:0002032,CL:0002320,CL:0002371
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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 16:57, 29 March 2012


Name:chronic myelogenous leukemia (CML) cell line:MEG-A2
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
age20
cell typemyeloid progenitor cell
cell lineMEG-A2
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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-penis0.158
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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: CNhs11865

Jaspar motifP-value
MA0002.20.0468
MA0003.10.639
MA0004.10.0265
MA0006.10.347
MA0007.10.374
MA0009.10.119
MA0014.10.377
MA0017.10.021
MA0018.26.34631e-4
MA0019.10.252
MA0024.14.09819e-5
MA0025.10.162
MA0027.10.309
MA0028.13.64506e-8
MA0029.10.00348
MA0030.10.328
MA0031.10.815
MA0035.21.07742e-26
MA0038.10.00478
MA0039.20.807
MA0040.10.0519
MA0041.10.588
MA0042.10.723
MA0043.10.00863
MA0046.10.378
MA0047.20.24
MA0048.10.296
MA0050.10.688
MA0051.10.433
MA0052.17.41457e-6
MA0055.10.0431
MA0057.10.383
MA0058.10.036
MA0059.10.00136
MA0060.10.111
MA0061.10.893
MA0062.21.2231e-12
MA0065.20.0114
MA0066.10.993
MA0067.10.819
MA0068.10.114
MA0069.10.198
MA0070.10.997
MA0071.10.051
MA0072.10.551
MA0073.10.492
MA0074.10.459
MA0076.11.43931e-7
MA0077.10.317
MA0078.10.72
MA0079.20.974
MA0080.22.39504e-8
MA0081.10.00858
MA0083.10.00494
MA0084.10.36
MA0087.10.145
MA0088.10.00209
MA0090.10.00113
MA0091.10.761
MA0092.10.939
MA0093.10.0371
MA0099.24.30153e-7
MA0100.11.24685e-4
MA0101.10.358
MA0102.20.152
MA0103.10.551
MA0104.21.4395e-4
MA0105.10.153
MA0106.10.924
MA0107.10.0652
MA0108.24.56464e-7
MA0111.10.167
MA0112.20.235
MA0113.10.836
MA0114.10.0374
MA0115.10.12
MA0116.10.00657
MA0117.10.497
MA0119.10.839
MA0122.10.534
MA0124.10.366
MA0125.10.25
MA0131.10.521
MA0135.10.994
MA0136.13.49565e-9
MA0137.20.523
MA0138.20.766
MA0139.10.971
MA0140.11.38422e-33
MA0141.10.161
MA0142.10.532
MA0143.10.319
MA0144.10.955
MA0145.10.475
MA0146.10.024
MA0147.13.53317e-5
MA0148.10.0616
MA0149.10.0444
MA0150.10.348
MA0152.10.192
MA0153.10.0443
MA0154.10.363
MA0155.10.933
MA0156.11.69085e-8
MA0157.10.93
MA0159.10.512
MA0160.10.0354
MA0162.10.849
MA0163.16.05192e-12
MA0164.10.819
MA0258.10.209
MA0259.10.0682



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: CNhs11865

Novel motifP-value
10.0686
100.0158
1000.66
1010.668
1020.374
1030.184
1040.673
1050.575
1060.976
1070.828
1080.581
1090.0125
110.0487
1100.396
1110.0318
1120.399
1130.581
1140.134
1150.135
1160.103
1170.0442
1180.132
1190.355
120.774
1200.59
1210.7
1220.937
1230.00784
1240.576
1250.0738
1260.544
1270.0865
1280.887
1290.721
130.00524
1300.565
1310.38
1320.659
1330.0449
1340.67
1350.396
1360.0588
1370.939
1380.951
1390.6
140.741
1400.505
1410.293
1420.434
1430.142
1440.692
1450.731
1460.801
1470.0513
1480.956
1490.167
150.235
1500.812
1510.816
1520.677
1530.842
1540.816
1550.0715
1560.819
1570.442
1580.601
1590.0968
160.957
1600.432
1610.287
1620.873
1630.284
1640.0938
1650.438
1660.163
1670.456
1680.861
1690.548
170.97
180.203
190.923
20.515
200.222
210.343
220.656
230.017
240.37
250.322
260.0938
270.948
280.738
290.0185
30.174
300.00941
310.368
320.0143
330.408
340.758
350.663
360.0335
370.271
380.364
390.42
40.294
400.315
410.345
420.396
430.62
440.791
450.686
460.321
470.0539
480.13
490.263
50.919
500.662
510.532
520.764
530.267
540.549
550.198
560.868
570.207
580.159
590.639
60.409
600.558
610.151
620.309
630.614
640.234
650.807
660.0264
670.992
680.123
690.824
70.0494
700.984
710.168
720.433
730.398
740.322
750.0118
760.161
770.376
780.00288
790.00635
80.134
800.49
810.553
820.33
830.576
840.591
850.0353
860.913
870.0219
880.198
890.687
90.93
900.0905
910.753
920.62
930.834
940.7
950.00407
960.635
970.448
980.0465
990.469



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: CNhs11865


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)
8552 (chronic myeloid leukemia)
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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