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FF:11931-125I5: 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 17:38, 29 March 2012


Name:CD34 cells differentiated to erythrocyte lineage, biol_ rep1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueBuffy coat
dev stageAdult
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationKim Summers
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.0763
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-lymphoma0.977
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs13552

Jaspar motifP-value
MA0002.20.382
MA0003.10.562
MA0004.10.841
MA0006.10.81
MA0007.10.788
MA0009.10.222
MA0014.10.875
MA0017.10.266
MA0018.20.993
MA0019.10.813
MA0024.13.4061e-10
MA0025.10.832
MA0027.10.527
MA0028.10.0123
MA0029.10.0234
MA0030.10.844
MA0031.10.0975
MA0035.21.28757e-37
MA0038.10.955
MA0039.20.935
MA0040.10.196
MA0041.10.5
MA0042.10.958
MA0043.10.421
MA0046.10.561
MA0047.20.414
MA0048.10.601
MA0050.10.668
MA0051.10.356
MA0052.10.0125
MA0055.10.12
MA0057.10.899
MA0058.10.55
MA0059.10.374
MA0060.17.06474e-9
MA0061.10.843
MA0062.20.0085
MA0065.20.00925
MA0066.10.122
MA0067.10.768
MA0068.10.00291
MA0069.10.439
MA0070.10.931
MA0071.10.248
MA0072.10.983
MA0073.10.851
MA0074.10.71
MA0076.15.08273e-4
MA0077.10.0908
MA0078.10.206
MA0079.20.0676
MA0080.20.0488
MA0081.10.886
MA0083.10.00264
MA0084.10.558
MA0087.10.17
MA0088.10.00899
MA0090.10.0838
MA0091.10.13
MA0092.10.642
MA0093.10.883
MA0099.20.128
MA0100.10.00372
MA0101.10.244
MA0102.20.112
MA0103.10.427
MA0104.20.16
MA0105.10.00479
MA0106.10.504
MA0107.10.0409
MA0108.20.00677
MA0111.10.191
MA0112.20.0181
MA0113.10.776
MA0114.10.0989
MA0115.10.115
MA0116.14.04889e-6
MA0117.10.441
MA0119.10.0913
MA0122.10.725
MA0124.10.402
MA0125.10.298
MA0131.10.257
MA0135.10.0311
MA0136.10.683
MA0137.20.522
MA0138.20.9
MA0139.10.24
MA0140.11.41363e-85
MA0141.10.0414
MA0142.10.507
MA0143.10.416
MA0144.10.327
MA0145.10.994
MA0146.10.414
MA0147.10.116
MA0148.10.275
MA0149.10.0301
MA0150.10.00173
MA0152.10.767
MA0153.10.336
MA0154.10.0547
MA0155.10.445
MA0156.10.482
MA0157.10.137
MA0159.10.313
MA0160.10.136
MA0162.10.916
MA0163.15.38847e-8
MA0164.10.83
MA0258.10.0484
MA0259.10.428



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: CNhs13552

Novel motifP-value
10.0091
100.0194
1000.331
1010.064
1020.766
1030.201
1040.719
1050.55
1060.892
1070.147
1080.22
1090.0378
110.0605
1100.209
1110.142
1120.476
1130.913
1140.193
1150.0339
1160.425
1170.035
1180.436
1190.976
120.212
1200.431
1210.48
1220.394
1230.0642
1240.429
1250.222
1260.75
1270.217
1280.981
1290.698
130.0219
1300.923
1310.528
1320.0492
1330.0402
1340.821
1350.779
1360.408
1370.769
1380.986
1390.908
140.742
1400.508
1410.115
1420.942
1430.199
1440.355
1450.931
1460.972
1470.115
1480.47
1490.718
150.045
1500.94
1510.654
1520.0876
1530.486
1540.565
1550.0282
1560.219
1570.271
1580.891
1590.0952
160.378
1600.741
1610.18
1620.648
1630.199
1640.38
1650.0861
1660.558
1670.286
1680.862
1690.728
170.792
180.555
190.658
20.464
200.169
210.108
220.85
230.256
240.244
250.0956
260.205
270.736
280.415
290.0142
30.232
300.0882
310.998
320.213
330.162
340.525
350.182
360.0257
370.355
380.322
390.637
40.875
400.203
410.446
420.188
430.212
440.603
450.695
460.0953
470.0272
480.164
490.0407
50.245
500.57
510.898
520.608
530.554
540.777
550.96
560.807
570.0323
580.199
590.906
60.44
600.95
610.699
620.0587
630.831
640.352
650.888
660.0134
670.74
680.188
690.218
70.0692
700.989
710.0295
720.767
730.973
740.666
750.00689
760.473
770.961
780.00552
790.173
80.366
800.939
810.656
820.463
830.426
840.544
850.473
860.636
870.453
880.88
890.986
90.893
900.0195
910.613
920.823
930.121
940.393
950.0771
960.0969
970.443
980.0712
990.0837



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: CNhs13552


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)
0000038 (erythroid progenitor cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000050 (megakaryocyte-erythroid progenitor cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000547 (proerythroblast)
0000548 (animal cell)
0000549 (basophilic erythroblast)
0000550 (polychromatophilic erythroblast)
0000552 (orthochromatic erythroblast)
0000558 (reticulocyte)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000764 (erythroid lineage cell)
0000765 (erythroblast)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
0007023 (adult organism)

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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