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FF:11305-117B9: 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 17:02, 29 March 2012


Name:CD14+ 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 stage57 years old adult
sexmale
age57
cell typemonocyte
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMon726
catalog number3H100-30-10
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-Peripheral0.506
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-Basophils0.0794
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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-Whole0.227
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-Whole0.256
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: CNhs11954

Jaspar motifP-value
MA0002.22.39706e-9
MA0003.10.679
MA0004.10.686
MA0006.10.755
MA0007.10.666
MA0009.10.085
MA0014.10.696
MA0017.10.512
MA0018.20.00772
MA0019.10.302
MA0024.10.00562
MA0025.13.54925e-4
MA0027.10.729
MA0028.10.0269
MA0029.10.219
MA0030.10.676
MA0031.10.661
MA0035.20.203
MA0038.10.218
MA0039.20.42
MA0040.10.607
MA0041.10.416
MA0042.10.595
MA0043.11.56641e-10
MA0046.10.00516
MA0047.20.72
MA0048.10.551
MA0050.12.58033e-7
MA0051.10.00211
MA0052.10.00682
MA0055.10.766
MA0057.10.208
MA0058.10.573
MA0059.10.673
MA0060.11.3738e-9
MA0061.11.41317e-30
MA0062.20.274
MA0065.20.111
MA0066.10.0821
MA0067.14.58986e-6
MA0068.10.362
MA0069.10.975
MA0070.10.0314
MA0071.10.34
MA0072.10.583
MA0073.10.39
MA0074.10.106
MA0076.10.0714
MA0077.10.209
MA0078.10.746
MA0079.20.394
MA0080.23.06951e-13
MA0081.12.47565e-4
MA0083.10.401
MA0084.10.951
MA0087.10.815
MA0088.10.18
MA0090.10.149
MA0091.10.602
MA0092.10.484
MA0093.10.843
MA0099.25.20307e-45
MA0100.10.553
MA0101.13.96281e-31
MA0102.22.44463e-11
MA0103.10.0431
MA0104.20.589
MA0105.11.95546e-27
MA0106.10.401
MA0107.11.05229e-36
MA0108.20.0166
MA0111.10.57
MA0112.20.00873
MA0113.10.595
MA0114.10.81
MA0115.10.259
MA0116.10.00369
MA0117.10.0155
MA0119.10.559
MA0122.10.729
MA0124.10.756
MA0125.10.0695
MA0131.10.557
MA0135.10.604
MA0136.12.99617e-14
MA0137.20.874
MA0138.20.0202
MA0139.10.312
MA0140.10.076
MA0141.10.281
MA0142.10.669
MA0143.10.568
MA0144.10.328
MA0145.10.855
MA0146.10.225
MA0147.10.738
MA0148.10.941
MA0149.10.553
MA0150.14.22643e-18
MA0152.10.216
MA0153.10.00122
MA0154.13.8029e-4
MA0155.10.945
MA0156.12.05425e-9
MA0157.10.457
MA0159.10.121
MA0160.10.0956
MA0162.10.785
MA0163.12.47297e-5
MA0164.10.477
MA0258.10.0496
MA0259.10.643



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: CNhs11954

Novel motifP-value
10.339
100.0132
1000.694
1010.992
1020.952
1030.677
1040.489
1050.111
1065.49669e-4
1070.32
1080.621
1090.435
110.417
1100.425
1110.0661
1120.579
1130.161
1140.125
1150.172
1160.691
1170.0623
1180.167
1190.472
120.234
1200.292
1210.633
1220.698
1230.00612
1240.751
1250.341
1260.204
1270.775
1280.0775
1290.955
130.166
1300.181
1310.966
1320.0527
1330.498
1340.808
1350.613
1360.932
1370.0117
1380.278
1390.0625
140.33
1400.255
1410.398
1420.248
1430.0319
1440.624
1450.609
1460.738
1470.47
1480.0464
1490.796
150.185
1500.581
1510.192
1520.243
1530.744
1540.413
1550.467
1560.574
1570.467
1580.0173
1590.486
160.787
1600.738
1610.549
1620.0987
1630.189
1640.0586
1650.29
1660.594
1670.225
1680.135
1690.0527
170.346
180.233
190.827
20.35
200.259
210.869
220.424
230.0509
240.758
250.357
260.176
270.521
280.41
290.269
30.259
300.228
310.877
320.12
330.335
340.705
350.134
360.0999
370.162
380.484
390.8
40.864
400.24
410.0057
420.456
430.0282
440.448
450.99
460.352
470.899
480.821
490.0899
50.251
500.9
510.475
520.402
530.201
540.534
550.933
560.918
570.832
580.204
590.514
60.936
600.0629
610.444
620.13
630.717
640.607
650.305
660.0459
670.629
680.214
690.205
70.262
700.0728
710.0543
720.252
730.209
740.0439
750.211
760.0681
770.998
780.256
790.619
80.955
800.122
810.406
820.255
830.284
840.0385
850.0558
860.0441
870.864
880.871
890.917
90.409
900.264
910.303
920.362
930.727
940.0853
950.262
960.461
970.757
980.135
990.00562



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: CNhs11954


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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