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FF:11625-122B5: 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 17:14, 29 March 2012


Name:CD34+ Progenitors, 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 stageNA
sexNA
ageNA
cell typehematopoietic stem cell, CD34+
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:c1
catalog number3H100-60-5
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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-Peripheral0.193
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-penis-0.0475
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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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-Whole0.193
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: CNhs12205

Jaspar motifP-value
MA0002.22.47049e-8
MA0003.10.779
MA0004.10.686
MA0006.10.263
MA0007.10.23
MA0009.10.149
MA0014.10.682
MA0017.10.992
MA0018.25.02871e-8
MA0019.10.652
MA0024.10.365
MA0025.11.24602e-5
MA0027.10.288
MA0028.10.449
MA0029.10.757
MA0030.10.0613
MA0031.10.0281
MA0035.20.126
MA0038.10.605
MA0039.20.517
MA0040.10.45
MA0041.10.0981
MA0042.10.169
MA0043.11.8446e-14
MA0046.10.216
MA0047.20.524
MA0048.10.927
MA0050.13.63388e-11
MA0051.16.03131e-7
MA0052.14.58402e-4
MA0055.10.928
MA0057.10.119
MA0058.10.309
MA0059.10.892
MA0060.10.0416
MA0061.11.32531e-47
MA0062.21.95534e-9
MA0065.20.39
MA0066.10.64
MA0067.13.60304e-8
MA0068.10.0225
MA0069.10.185
MA0070.10.416
MA0071.10.514
MA0072.10.307
MA0073.10.224
MA0074.10.362
MA0076.10.0676
MA0077.10.305
MA0078.10.432
MA0079.20.646
MA0080.25.70626e-13
MA0081.11.43404e-4
MA0083.10.517
MA0084.10.467
MA0087.10.934
MA0088.10.224
MA0090.10.0139
MA0091.10.371
MA0092.10.752
MA0093.10.692
MA0099.29.47244e-34
MA0100.10.0994
MA0101.11.04228e-46
MA0102.27.0999e-10
MA0103.10.0244
MA0104.20.217
MA0105.11.00664e-21
MA0106.10.0417
MA0107.11.32561e-51
MA0108.20.624
MA0111.10.798
MA0112.20.955
MA0113.10.382
MA0114.10.471
MA0115.10.248
MA0116.10.0482
MA0117.10.00111
MA0119.10.258
MA0122.10.538
MA0124.10.237
MA0125.10.231
MA0131.10.789
MA0135.10.486
MA0136.12.99114e-18
MA0137.20.0343
MA0138.20.0347
MA0139.10.513
MA0140.10.057
MA0141.10.792
MA0142.10.712
MA0143.10.798
MA0144.10.179
MA0145.10.164
MA0146.10.658
MA0147.10.481
MA0148.10.601
MA0149.10.861
MA0150.14.59935e-13
MA0152.10.239
MA0153.10.0106
MA0154.10.00325
MA0155.10.816
MA0156.13.48014e-18
MA0157.10.0736
MA0159.10.384
MA0160.10.121
MA0162.10.322
MA0163.10.00484
MA0164.10.955
MA0258.10.854
MA0259.10.881



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: CNhs12205

Novel motifP-value
10.841
100.127
1000.173
1010.953
1020.951
1030.563
1040.434
1050.0978
1060.0123
1070.564
1080.232
1090.698
110.657
1100.936
1110.759
1120.946
1130.213
1140.908
1150.162
1160.213
1170.0384
1180.302
1190.434
120.347
1200.416
1210.4
1220.281
1230.696
1240.589
1250.959
1260.0668
1270.781
1280.389
1290.556
130.185
1300.8
1310.442
1320.0173
1330.34
1340.905
1350.938
1360.845
1370.0158
1380.73
1390.227
140.528
1400.589
1410.545
1420.17
1430.0133
1440.943
1450.713
1460.983
1470.15
1480.348
1490.302
150.302
1500.531
1510.785
1520.558
1530.895
1540.575
1550.285
1560.653
1570.679
1580.03
1590.0995
160.659
1600.337
1610.625
1620.00826
1630.417
1640.169
1650.42
1660.796
1670.328
1680.138
1690.255
170.915
180.558
190.0838
20.209
200.211
210.685
220.785
230.48
240.723
250.267
260.676
270.387
280.261
290.161
30.73
300.263
310.761
324.80792e-4
330.283
340.785
350.169
360.208
370.152
380.91
390.779
40.895
400.65
410.0111
420.519
430.129
440.397
450.879
460.833
470.899
480.805
490.396
50.477
500.687
510.685
520.707
530.591
540.915
550.523
560.776
570.561
580.217
590.751
60.718
600.215
610.369
620.229
630.536
640.983
650.874
660.336
670.89
680.433
690.0946
70.353
700.617
710.26
720.193
730.43
740.0632
750.276
760.178
770.135
780.409
790.128
80.353
800.0132
810.919
820.647
830.00226
840.0657
850.71
860.0511
870.216
880.606
890.306
90.436
900.807
910.998
920.949
930.35
940.208
950.0897
960.886
970.943
980.312
995.93318e-6



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: CNhs12205


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)

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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