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|rna_box=110
|rna_box=110

Revision as of 17:01, 21 September 2012


Name:chronic myeloblastic leukemia (CML) cell line:KCL-22
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
age28
cell typegranulocyte monocyte progenitor cell
cell lineKCL-22
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-penis0.147
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-lymphoma0.481
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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



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: CNhs11886

Jaspar motifP-value
MA0002.27.49377e-5
MA0003.10.658
MA0004.10.036
MA0006.10.17
MA0007.10.179
MA0009.10.409
MA0014.10.67
MA0017.10.026
MA0018.20.0121
MA0019.10.0342
MA0024.16.46613e-5
MA0025.10.0994
MA0027.10.263
MA0028.14.14704e-5
MA0029.10.301
MA0030.10.0555
MA0031.10.124
MA0035.20.00603
MA0038.13.62458e-4
MA0039.20.372
MA0040.10.527
MA0041.10.158
MA0042.10.391
MA0043.10.0128
MA0046.10.514
MA0047.20.0754
MA0048.10.0952
MA0050.10.18
MA0051.10.0698
MA0052.10.117
MA0055.10.00826
MA0057.10.287
MA0058.10.0226
MA0059.12.13901e-5
MA0060.10.0388
MA0061.10.616
MA0062.21.28291e-9
MA0065.20.00412
MA0066.10.702
MA0067.10.897
MA0068.10.774
MA0069.10.124
MA0070.10.807
MA0071.10.162
MA0072.10.529
MA0073.10.426
MA0074.10.997
MA0076.11.35297e-4
MA0077.10.111
MA0078.10.988
MA0079.20.578
MA0080.22.80547e-10
MA0081.10.0153
MA0083.10.0791
MA0084.10.674
MA0087.10.354
MA0088.19.11423e-4
MA0090.16.59444e-4
MA0091.10.67
MA0092.10.889
MA0093.10.0279
MA0099.20.00701
MA0100.10.00334
MA0101.10.306
MA0102.20.652
MA0103.10.584
MA0104.23.5745e-5
MA0105.10.207
MA0106.10.378
MA0107.10.0189
MA0108.25.53959e-6
MA0111.10.724
MA0112.20.384
MA0113.10.985
MA0114.10.131
MA0115.10.146
MA0116.11.2672e-4
MA0117.10.872
MA0119.10.282
MA0122.10.519
MA0124.10.766
MA0125.10.848
MA0131.10.0811
MA0135.10.728
MA0136.12.15417e-15
MA0137.20.227
MA0138.20.714
MA0139.10.108
MA0140.10.00167
MA0141.10.0261
MA0142.10.409
MA0143.10.757
MA0144.10.385
MA0145.10.188
MA0146.10.00213
MA0147.11.16615e-6
MA0148.10.0293
MA0149.10.0481
MA0150.10.948
MA0152.10.92
MA0153.10.099
MA0154.10.077
MA0155.10.94
MA0156.11.92247e-12
MA0157.10.896
MA0159.10.962
MA0160.10.012
MA0162.10.624
MA0163.13.02869e-13
MA0164.10.806
MA0258.10.183
MA0259.10.0163



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: CNhs11886

Novel motifP-value
10.14
100.00648
1000.58
1010.737
1020.404
1030.83
1040.804
1050.966
1060.68
1070.837
1080.501
1090.0793
110.0515
1100.118
1110.0802
1120.586
1130.987
1140.0376
1150.807
1160.197
1170.0133
1180.0319
1190.897
120.886
1200.274
1210.833
1220.843
1230.00771
1240.466
1250.24
1260.493
1270.0801
1280.465
1290.695
130.00211
1300.795
1310.389
1320.622
1330.622
1340.917
1350.596
1360.204
1370.459
1380.279
1390.978
140.891
1400.333
1410.114
1420.482
1430.212
1440.295
1450.206
1460.623
1470.00872
1480.0601
1490.221
150.255
1500.705
1510.79
1520.663
1530.595
1540.892
1550.0387
1560.27
1570.167
1580.869
1590.364
160.397
1600.386
1610.18
1620.455
1630.999
1640.111
1650.527
1660.0499
1670.173
1680.107
1690.0307
170.858
180.206
190.923
20.568
200.218
210.302
220.387
230.0428
240.184
250.144
260.0237
270.816
280.853
290.12
30.144
300.1
310.187
320.00978
330.502
340.749
350.659
360.0653
370.251
380.41
390.212
40.284
400.347
410.86
420.259
430.607
440.0218
450.42
460.0739
470.0299
480.00765
490.249
50.757
500.955
510.655
520.0973
530.123
540.975
550.109
560.95
570.035
580.13
590.469
60.333
600.777
610.0437
620.158
630.554
640.136
650.761
660.0533
670.471
680.908
690.871
70.0395
700.882
710.0317
720.683
730.179
740.654
750.0101
760.0648
770.844
780.0722
790.393
80.0556
800.0787
810.646
820.981
830.398
840.339
850.232
860.783
870.127
880.446
890.625
90.749
900.496
910.666
920.281
930.438
940.935
950.00306
960.367
970.281
980.219
990.557



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: CNhs11886


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)
1036 (chronic leukemia)
8692 (myeloid leukemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100737 (leukemia cell line sample)
0102580 (chronic myeloid leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0100740 (myeloid leukemia cell line sample)
0104137 (KCL-22 cell sample)

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
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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