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FF:11799-124C8: 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 17:30, 29 March 2012


Name:CD14+CD16- Monocytes, 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
sexmale
age23
cell typemonocyte
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number27
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-0.135
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.162
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.396
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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-Whole0.243
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: CNhs13216

Jaspar motifP-value
MA0002.24.09245e-10
MA0003.10.111
MA0004.10.853
MA0006.10.854
MA0007.10.77
MA0009.10.21
MA0014.10.642
MA0017.10.0107
MA0018.20.156
MA0019.10.282
MA0024.10.00126
MA0025.10.00344
MA0027.10.978
MA0028.10.942
MA0029.10.169
MA0030.10.326
MA0031.10.805
MA0035.20.317
MA0038.10.109
MA0039.20.644
MA0040.10.153
MA0041.10.589
MA0042.10.298
MA0043.17.75373e-6
MA0046.10.247
MA0047.20.206
MA0048.10.881
MA0050.16.18011e-9
MA0051.14.58173e-4
MA0052.10.661
MA0055.10.714
MA0057.10.607
MA0058.10.685
MA0059.10.617
MA0060.12.46086e-9
MA0061.12.99399e-5
MA0062.20.00651
MA0065.20.0135
MA0066.10.0624
MA0067.15.84643e-4
MA0068.10.928
MA0069.10.891
MA0070.10.00651
MA0071.10.241
MA0072.10.897
MA0073.10.415
MA0074.10.378
MA0076.10.829
MA0077.10.119
MA0078.10.865
MA0079.20.594
MA0080.26.54416e-17
MA0081.11.04644e-4
MA0083.10.323
MA0084.10.615
MA0087.10.492
MA0088.10.621
MA0090.10.0512
MA0091.10.467
MA0092.10.449
MA0093.10.962
MA0099.21.38051e-9
MA0100.10.975
MA0101.13.07648e-4
MA0102.28.92754e-12
MA0103.10.439
MA0104.20.681
MA0105.11.03562e-7
MA0106.10.448
MA0107.16.86641e-5
MA0108.26.29609e-8
MA0111.10.397
MA0112.24.39556e-4
MA0113.10.998
MA0114.10.129
MA0115.10.964
MA0116.11.25275e-4
MA0117.10.225
MA0119.10.364
MA0122.10.827
MA0124.10.345
MA0125.10.183
MA0131.10.985
MA0135.10.337
MA0136.12.62167e-18
MA0137.20.567
MA0138.20.9
MA0139.10.737
MA0140.10.33
MA0141.10.0663
MA0142.10.438
MA0143.10.484
MA0144.10.215
MA0145.10.228
MA0146.10.0395
MA0147.10.773
MA0148.10.956
MA0149.10.0891
MA0150.11.36404e-6
MA0152.10.213
MA0153.10.0183
MA0154.10.00171
MA0155.10.8
MA0156.15.50106e-11
MA0157.10.294
MA0159.10.0397
MA0160.10.0353
MA0162.10.429
MA0163.14.03478e-9
MA0164.10.899
MA0258.10.0111
MA0259.10.744



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: CNhs13216

Novel motifP-value
10.105
100.0189
1000.979
1010.385
1020.575
1030.214
1040.794
1050.266
1060.00483
1070.354
1080.706
1090.0652
110.116
1100.288
1110.027
1120.256
1130.533
1140.0112
1150.125
1160.757
1170.0353
1180.1
1190.29
120.323
1200.66
1210.871
1220.801
1230.0291
1240.827
1250.11
1260.289
1270.258
1280.0372
1290.796
130.101
1300.202
1310.839
1320.0605
1330.972
1340.478
1350.0698
1360.879
1371.80623e-4
1380.136
1390.0377
140.289
1400.151
1410.332
1420.974
1430.0435
1440.705
1450.498
1460.814
1470.289
1480.00641
1490.654
150.0999
1500.61
1510.293
1520.284
1530.69
1540.649
1550.283
1560.918
1570.755
1580.116
1590.831
160.381
1600.371
1610.398
1620.445
1630.839
1640.0973
1650.111
1660.756
1670.181
1680.345
1690.00866
170.28
180.164
190.2
20.993
200.604
210.512
220.219
230.125
240.192
250.173
260.0292
270.485
280.548
290.0701
30.0637
300.52
310.667
320.79
330.194
340.486
350.136
360.0476
370.0641
380.427
390.734
40.885
400.103
410.0283
420.327
430.0786
440.774
450.859
460.151
470.388
480.365
490.118
50.106
500.986
510.317
520.343
530.22
540.374
550.505
560.741
570.656
580.081
590.136
60.59
600.0418
610.248
620.0293
630.473
640.317
650.216
660.127
670.472
680.774
690.719
70.136
700.0169
710.0214
720.289
730.139
740.0497
750.0702
760.222
770.464
780.149
790.0392
80.359
800.26
810.255
820.0733
830.536
840.581
850.0276
860.105
870.234
880.591
890.349
90.289
900.0405
910.35
920.336
930.486
940.0308
950.119
960.401
970.968
980.156
990.0481



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: CNhs13216


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)

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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