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FF:11545-120B6: 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 17:31, 29 March 2012


Name:CD34+ Progenitors, donor1
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 numberNA
catalog number3H100-60-5
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis-0.169
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-lymphoma-0.243
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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: CNhs13227

Jaspar motifP-value
MA0002.21.10396e-7
MA0003.10.331
MA0004.10.664
MA0006.10.333
MA0007.10.39
MA0009.10.897
MA0014.10.965
MA0017.10.967
MA0018.21.7311e-11
MA0019.10.89
MA0024.10.924
MA0025.14.31339e-5
MA0027.10.648
MA0028.10.0327
MA0029.10.161
MA0030.12.66324e-4
MA0031.13.48666e-4
MA0035.27.51241e-5
MA0038.10.369
MA0039.20.312
MA0040.10.0118
MA0041.10.065
MA0042.10.0444
MA0043.17.65114e-12
MA0046.10.638
MA0047.20.0483
MA0048.10.572
MA0050.12.28765e-5
MA0051.15.44299e-4
MA0052.14.44722e-5
MA0055.10.629
MA0057.10.268
MA0058.10.69
MA0059.10.985
MA0060.10.807
MA0061.12.45653e-19
MA0062.21.47048e-9
MA0065.20.232
MA0066.10.591
MA0067.12.94381e-7
MA0068.14.80945e-4
MA0069.10.0878
MA0070.10.938
MA0071.10.737
MA0072.10.639
MA0073.10.242
MA0074.10.968
MA0076.10.00383
MA0077.10.608
MA0078.10.31
MA0079.20.398
MA0080.22.79502e-14
MA0081.12.95621e-4
MA0083.10.589
MA0084.10.297
MA0087.10.805
MA0088.10.836
MA0090.14.35626e-4
MA0091.10.483
MA0092.10.703
MA0093.10.718
MA0099.26.9392e-8
MA0100.10.00113
MA0101.15.87277e-24
MA0102.26.18505e-5
MA0103.10.45
MA0104.20.0378
MA0105.11.67038e-10
MA0106.10.0877
MA0107.14.52226e-24
MA0108.20.68
MA0111.10.402
MA0112.20.76
MA0113.10.269
MA0114.10.942
MA0115.10.286
MA0116.10.0269
MA0117.10.014
MA0119.10.596
MA0122.10.311
MA0124.10.708
MA0125.10.447
MA0131.10.283
MA0135.10.592
MA0136.12.06507e-19
MA0137.20.0321
MA0138.20.155
MA0139.10.7
MA0140.12.13483e-5
MA0141.10.377
MA0142.10.395
MA0143.10.687
MA0144.10.292
MA0145.10.432
MA0146.10.764
MA0147.10.0754
MA0148.10.149
MA0149.10.943
MA0150.16.82401e-6
MA0152.10.165
MA0153.10.377
MA0154.10.00291
MA0155.10.247
MA0156.18.75163e-17
MA0157.10.0623
MA0159.10.746
MA0160.10.0646
MA0162.10.912
MA0163.17.41339e-4
MA0164.10.584
MA0258.10.56
MA0259.10.673



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: CNhs13227

Novel motifP-value
10.672
100.125
1000.389
1010.627
1020.885
1030.185
1040.424
1050.446
1060.00505
1070.273
1080.216
1090.321
110.599
1100.564
1110.14
1120.892
1130.366
1140.606
1150.262
1160.297
1170.0039
1180.114
1190.372
120.285
1200.592
1210.529
1220.345
1230.546
1240.903
1250.939
1260.298
1270.798
1280.451
1290.867
130.153
1300.691
1310.579
1320.0192
1330.0297
1340.598
1350.873
1360.359
1370.00204
1380.771
1390.413
140.85
1400.47
1410.821
1420.862
1430.13
1440.721
1450.281
1460.86
1470.0656
1480.815
1490.866
150.402
1500.654
1510.562
1520.258
1530.866
1540.811
1550.0354
1560.307
1570.309
1580.0586
1590.129
160.596
1600.476
1610.364
1620.0798
1630.866
1640.587
1650.35
1660.526
1670.221
1680.755
1690.339
170.822
180.723
190.187
20.326
200.35
210.247
220.953
230.952
240.935
250.35
260.968
270.748
280.371
290.134
30.647
300.422
310.662
320.0138
330.291
340.776
350.258
360.156
370.00893
380.784
390.739
40.592
400.69
410.0984
420.436
430.702
440.372
450.938
460.764
470.747
480.918
490.541
50.544
500.985
510.518
520.682
530.672
540.662
550.463
560.978
570.528
580.288
590.563
60.272
600.343
610.0767
620.214
630.634
640.87
650.596
660.912
670.656
680.975
690.215
70.5
700.691
710.166
720.141
730.123
740.528
750.186
760.303
770.0784
780.965
790.0633
80.341
800.0206
810.814
820.107
830.0033
840.322
850.953
860.0284
870.0556
880.518
890.106
90.306
900.983
910.783
920.949
930.511
940.377
950.0022
960.63
970.967
980.487
995.00058e-5



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: CNhs13227


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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