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FF:11789-124B7: 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 17:37, 29 March 2012


Name:CD14+CD16+ Monocytes, 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
sexmale
age25
cell typemonocyte
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number7
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-penis-0.127
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.0832
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.309
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.768
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: CNhs13541

Jaspar motifP-value
MA0002.21.49857e-9
MA0003.10.0473
MA0004.10.353
MA0006.10.9
MA0007.10.883
MA0009.10.407
MA0014.10.546
MA0017.10.00653
MA0018.20.0693
MA0019.10.802
MA0024.10.00538
MA0025.10.00283
MA0027.10.756
MA0028.10.657
MA0029.10.138
MA0030.10.385
MA0031.10.834
MA0035.20.697
MA0038.10.169
MA0039.20.575
MA0040.10.152
MA0041.10.421
MA0042.10.0802
MA0043.13.89752e-4
MA0046.10.0571
MA0047.20.222
MA0048.10.947
MA0050.11.08004e-11
MA0051.15.18284e-6
MA0052.10.154
MA0055.10.801
MA0057.10.945
MA0058.10.226
MA0059.10.342
MA0060.19.52541e-7
MA0061.12.29714e-5
MA0062.29.26628e-4
MA0065.20.00825
MA0066.10.0423
MA0067.15.81292e-4
MA0068.10.23
MA0069.10.855
MA0070.10.00789
MA0071.10.114
MA0072.10.78
MA0073.10.317
MA0074.10.331
MA0076.10.736
MA0077.10.0662
MA0078.10.886
MA0079.20.509
MA0080.28.73293e-16
MA0081.11.4373e-4
MA0083.10.457
MA0084.10.384
MA0087.10.43
MA0088.10.567
MA0090.10.04
MA0091.10.392
MA0092.10.439
MA0093.10.405
MA0099.27.54705e-8
MA0100.10.867
MA0101.11.27021e-4
MA0102.24.17424e-8
MA0103.10.269
MA0104.20.267
MA0105.11.58763e-7
MA0106.10.75
MA0107.17.98858e-6
MA0108.24.72456e-6
MA0111.10.351
MA0112.21.73873e-4
MA0113.10.785
MA0114.10.0914
MA0115.10.603
MA0116.17.42014e-5
MA0117.10.275
MA0119.10.386
MA0122.10.783
MA0124.10.486
MA0125.10.235
MA0131.10.879
MA0135.10.374
MA0136.14.97064e-19
MA0137.20.579
MA0138.20.97
MA0139.10.639
MA0140.10.828
MA0141.10.0141
MA0142.10.595
MA0143.10.916
MA0144.10.332
MA0145.10.193
MA0146.10.0622
MA0147.10.306
MA0148.10.49
MA0149.10.0566
MA0150.12.34119e-4
MA0152.10.0957
MA0153.10.00578
MA0154.10.00116
MA0155.10.718
MA0156.19.60269e-12
MA0157.10.485
MA0159.10.0291
MA0160.10.00812
MA0162.10.514
MA0163.13.68601e-11
MA0164.10.981
MA0258.10.00741
MA0259.10.911



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: CNhs13541

Novel motifP-value
10.108
100.0307
1000.97
1010.628
1020.55
1030.131
1040.521
1050.142
1060.0104
1070.545
1080.723
1090.0456
110.156
1100.29
1110.0359
1120.145
1130.654
1140.0112
1150.179
1160.986
1170.0545
1180.0963
1190.289
120.37
1200.516
1210.759
1220.657
1230.0697
1240.5
1250.138
1260.104
1270.294
1280.0873
1290.785
130.0941
1300.429
1310.949
1320.0309
1330.345
1340.668
1350.0544
1360.83
1372.0407e-4
1380.186
1390.0274
140.44
1400.166
1410.448
1420.66
1430.0308
1440.771
1450.523
1460.974
1470.451
1480.0233
1490.644
150.098
1500.665
1510.275
1520.288
1530.591
1540.94
1550.238
1560.95
1570.844
1580.17
1590.41
160.377
1600.432
1610.45
1620.312
1630.959
1640.104
1650.0554
1660.547
1670.177
1680.352
1690.0109
170.281
180.147
190.243
20.827
200.56
210.589
220.196
230.156
240.209
250.161
260.0425
270.423
280.588
290.0751
30.0959
300.502
310.658
320.831
330.18
340.49
350.172
360.0511
370.0682
380.434
390.835
40.985
400.11
410.0262
420.301
430.0667
440.538
450.815
460.115
470.399
480.38
490.119
50.114
500.944
510.324
520.432
530.376
540.461
550.571
560.772
570.803
580.0504
590.0916
60.758
600.0514
610.235
620.015
630.503
640.294
650.255
660.231
670.476
680.991
690.955
70.144
700.0195
710.0322
720.205
730.147
740.146
750.0545
760.261
770.474
780.185
790.217
80.324
800.211
810.201
820.126
830.332
840.791
850.0243
860.125
870.24
880.576
890.373
90.242
900.0739
910.26
920.31
930.452
940.0195
950.0759
960.331
970.923
980.111
990.0742



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: CNhs13541


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)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000860 (classical monocyte)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002057 (CD14-positive, CD16-negative classical monocyte)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002393 (intermediate monocyte)
0002397 (CD14-positive, CD16-positive monocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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