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FF:11932-125I6: 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_ rep2
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
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-lymphoma0.894
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13553

Jaspar motifP-value
MA0002.20.363
MA0003.10.656
MA0004.10.75
MA0006.10.87
MA0007.10.361
MA0009.10.376
MA0014.10.739
MA0017.10.194
MA0018.20.885
MA0019.10.854
MA0024.13.45536e-9
MA0025.10.748
MA0027.10.656
MA0028.10.0339
MA0029.10.0363
MA0030.10.937
MA0031.10.112
MA0035.21.43838e-38
MA0038.10.942
MA0039.20.961
MA0040.10.236
MA0041.10.482
MA0042.10.972
MA0043.10.463
MA0046.10.804
MA0047.20.512
MA0048.10.639
MA0050.10.977
MA0051.10.329
MA0052.10.0567
MA0055.10.116
MA0057.10.862
MA0058.10.551
MA0059.10.315
MA0060.11.29255e-8
MA0061.10.857
MA0062.20.0251
MA0065.20.00862
MA0066.10.0871
MA0067.10.605
MA0068.10.023
MA0069.10.49
MA0070.10.516
MA0071.10.205
MA0072.10.882
MA0073.10.765
MA0074.10.679
MA0076.10.0052
MA0077.10.139
MA0078.10.203
MA0079.20.0699
MA0080.20.0411
MA0081.10.922
MA0083.10.00884
MA0084.10.693
MA0087.10.165
MA0088.10.0125
MA0090.10.14
MA0091.10.112
MA0092.10.493
MA0093.10.824
MA0099.20.204
MA0100.10.00793
MA0101.10.294
MA0102.20.0575
MA0103.10.346
MA0104.20.117
MA0105.10.00437
MA0106.10.527
MA0107.10.0452
MA0108.20.0237
MA0111.10.231
MA0112.20.00813
MA0113.10.742
MA0114.10.0949
MA0115.10.107
MA0116.12.79206e-6
MA0117.10.48
MA0119.10.0546
MA0122.10.47
MA0124.10.369
MA0125.10.398
MA0131.10.367
MA0135.10.0388
MA0136.10.947
MA0137.20.477
MA0138.20.565
MA0139.10.339
MA0140.12.72394e-84
MA0141.10.0388
MA0142.10.424
MA0143.10.28
MA0144.10.438
MA0145.10.905
MA0146.10.272
MA0147.10.1
MA0148.10.355
MA0149.10.0195
MA0150.10.0011
MA0152.10.863
MA0153.10.483
MA0154.10.0364
MA0155.10.512
MA0156.10.784
MA0157.10.152
MA0159.10.306
MA0160.10.0869
MA0162.10.643
MA0163.15.84113e-10
MA0164.10.6
MA0258.10.0392
MA0259.10.411



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: CNhs13553

Novel motifP-value
10.0119
100.018
1000.286
1010.0563
1020.731
1030.28
1040.583
1050.492
1060.99
1070.194
1080.322
1090.025
110.039
1100.182
1110.271
1120.407
1130.837
1140.276
1150.0632
1160.408
1170.0361
1180.396
1190.841
120.235
1200.465
1210.696
1220.465
1230.0217
1240.354
1250.129
1260.906
1270.402
1280.768
1290.627
130.0335
1300.933
1310.787
1320.0923
1330.118
1340.721
1350.772
1360.366
1370.754
1380.957
1390.953
140.741
1400.468
1410.0767
1420.781
1430.172
1440.288
1450.808
1460.685
1470.106
1480.306
1490.933
150.0325
1500.933
1510.615
1520.133
1530.525
1540.468
1550.0616
1560.082
1570.322
1580.904
1590.0485
160.399
1600.62
1610.0913
1620.8
1630.0883
1640.296
1650.157
1660.932
1670.22
1680.822
1690.518
170.75
180.512
190.579
20.513
200.186
210.183
220.837
230.37
240.322
250.104
260.125
270.856
280.416
290.0124
30.19
300.101
310.899
320.255
330.184
340.572
350.22
360.0215
370.324
380.295
390.643
40.878
400.128
410.438
420.138
430.202
440.39
450.762
460.0877
470.0195
480.146
490.0459
50.257
500.606
510.88
520.662
530.457
540.865
550.869
560.621
570.0203
580.202
590.895
60.344
600.932
610.772
620.0604
630.737
640.276
650.726
660.0175
670.626
680.233
690.243
70.0627
700.818
710.0253
720.661
730.821
740.389
750.00759
760.527
770.999
780.0109
790.165
80.274
800.909
810.488
820.338
830.243
840.919
850.67
860.688
870.26
880.969
890.937
90.919
900.0232
910.685
920.823
930.185
940.3
950.0718
960.115
970.558
980.0549
990.107



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: CNhs13553


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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