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FF:11381-118B4: 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 17:05, 29 March 2012


Name:CD14+ Monocytes, donor3
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 stage53 years old adult
sexmale
age53
cell typemonocyte
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMon727
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-Peripheral0.47
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-Basophils0.0853
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.0892
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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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-Whole0.218
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-Whole0.271
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: CNhs11997

Jaspar motifP-value
MA0002.27.5738e-9
MA0003.10.747
MA0004.10.568
MA0006.10.594
MA0007.10.735
MA0009.10.0761
MA0014.10.901
MA0017.10.641
MA0018.20.00164
MA0019.10.248
MA0024.10.014
MA0025.18.65647e-5
MA0027.10.921
MA0028.10.0836
MA0029.10.126
MA0030.10.498
MA0031.10.522
MA0035.20.173
MA0038.10.308
MA0039.20.584
MA0040.10.624
MA0041.10.431
MA0042.10.731
MA0043.14.04295e-11
MA0046.10.00365
MA0047.20.697
MA0048.10.459
MA0050.12.43221e-8
MA0051.15.41572e-4
MA0052.10.0126
MA0055.10.434
MA0057.10.19
MA0058.10.452
MA0059.10.733
MA0060.18.23336e-8
MA0061.16.10043e-34
MA0062.20.0443
MA0065.20.199
MA0066.10.101
MA0067.19.94653e-7
MA0068.10.963
MA0069.10.827
MA0070.10.0365
MA0071.10.355
MA0072.10.558
MA0073.10.344
MA0074.10.136
MA0076.10.207
MA0077.10.209
MA0078.10.839
MA0079.20.465
MA0080.23.81109e-13
MA0081.12.44747e-4
MA0083.10.535
MA0084.10.678
MA0087.10.764
MA0088.10.2
MA0090.10.0966
MA0091.10.589
MA0092.10.621
MA0093.10.706
MA0099.23.01127e-46
MA0100.10.501
MA0101.18.09425e-34
MA0102.25.96745e-11
MA0103.10.0259
MA0104.20.575
MA0105.16.60762e-28
MA0106.10.234
MA0107.11.52921e-38
MA0108.20.0295
MA0111.10.592
MA0112.20.034
MA0113.10.493
MA0114.10.93
MA0115.10.131
MA0116.10.00632
MA0117.10.0195
MA0119.10.658
MA0122.10.849
MA0124.10.73
MA0125.10.0657
MA0131.10.853
MA0135.10.697
MA0136.11.10619e-14
MA0137.20.861
MA0138.20.0141
MA0139.10.242
MA0140.10.0605
MA0141.10.339
MA0142.10.631
MA0143.10.52
MA0144.10.33
MA0145.10.981
MA0146.10.234
MA0147.10.767
MA0148.10.975
MA0149.10.526
MA0150.13.65512e-19
MA0152.10.27
MA0153.10.00161
MA0154.17.14052e-4
MA0155.10.841
MA0156.11.71201e-10
MA0157.10.306
MA0159.10.145
MA0160.10.0944
MA0162.10.662
MA0163.17.77228e-5
MA0164.10.566
MA0258.10.0887
MA0259.10.749



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: CNhs11997

Novel motifP-value
10.384
100.0124
1000.844
1010.772
1020.931
1030.772
1040.456
1050.0884
1068.38751e-4
1070.483
1080.505
1090.419
110.443
1100.486
1110.0817
1120.708
1130.132
1140.217
1150.129
1160.671
1170.0314
1180.147
1190.581
120.183
1200.271
1210.558
1220.6
1230.00532
1240.614
1250.288
1260.268
1270.832
1280.0866
1290.888
130.133
1300.213
1310.81
1320.0702
1330.61
1340.847
1350.967
1360.968
1370.0054
1380.27
1390.0929
140.337
1400.396
1410.432
1420.243
1430.0416
1440.61
1450.508
1460.75
1470.442
1480.0578
1490.556
150.187
1500.676
1510.183
1520.209
1530.787
1540.403
1550.527
1560.725
1570.638
1580.0225
1590.268
160.922
1600.938
1610.751
1620.112
1630.155
1640.0538
1650.36
1660.558
1670.183
1680.154
1690.0818
170.448
180.316
190.936
20.23
200.191
210.927
220.475
230.0953
240.756
250.322
260.136
270.382
280.367
290.222
30.309
300.197
310.887
320.0819
330.27
340.695
350.146
360.075
370.147
380.534
390.87
40.72
400.201
410.00661
420.494
430.0353
440.313
450.88
460.484
470.954
480.85
490.0855
50.284
500.859
510.588
520.482
530.21
540.651
550.955
560.976
570.981
580.227
590.51
60.962
600.091
610.488
620.183
630.802
640.583
650.35
660.0423
670.651
680.281
690.304
70.288
700.0898
710.0457
720.238
730.142
740.0678
750.159
760.0445
770.923
780.375
790.79
80.953
800.115
810.425
820.402
830.335
840.0415
850.103
860.0276
870.762
880.785
890.756
90.475
900.28
910.384
920.587
930.692
940.103
950.228
960.593
970.722
980.13
990.00241



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: CNhs11997


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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