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FF:11878-125C6: 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 17:34, 29 March 2012


Name:CD14+ monocytes - treated with Candida, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age51
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD4-9
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-Peripheral0.973
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
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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-Whole0.216
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: CNhs13488

Jaspar motifP-value
MA0002.24.42545e-8
MA0003.10.94
MA0004.10.0712
MA0006.10.63
MA0007.10.908
MA0009.10.437
MA0014.10.805
MA0017.10.26
MA0018.20.0135
MA0019.10.567
MA0024.10.00545
MA0025.16.34523e-4
MA0027.10.956
MA0028.10.101
MA0029.10.116
MA0030.10.153
MA0031.10.356
MA0035.20.285
MA0038.10.695
MA0039.20.716
MA0040.10.79
MA0041.10.775
MA0042.10.433
MA0043.15.52544e-9
MA0046.10.012
MA0047.20.314
MA0048.10.53
MA0050.15.1182e-8
MA0051.10.00244
MA0052.17.75486e-4
MA0055.10.374
MA0057.10.304
MA0058.10.0119
MA0059.10.0489
MA0060.11.26584e-6
MA0061.11.2398e-15
MA0062.20.699
MA0065.20.0371
MA0066.10.0546
MA0067.12.08636e-7
MA0068.10.539
MA0069.10.837
MA0070.10.0226
MA0071.10.339
MA0072.10.473
MA0073.10.462
MA0074.10.106
MA0076.10.117
MA0077.10.314
MA0078.10.442
MA0079.20.133
MA0080.24.96701e-11
MA0081.15.44203e-4
MA0083.10.898
MA0084.10.578
MA0087.10.779
MA0088.10.587
MA0090.10.522
MA0091.10.762
MA0092.10.45
MA0093.10.0848
MA0099.24.43934e-46
MA0100.10.776
MA0101.15.55384e-17
MA0102.22.09136e-8
MA0103.10.0701
MA0104.20.0519
MA0105.15.20781e-22
MA0106.10.815
MA0107.13.78528e-20
MA0108.20.741
MA0111.10.542
MA0112.23.22518e-4
MA0113.10.829
MA0114.10.274
MA0115.10.549
MA0116.17.35272e-4
MA0117.10.0245
MA0119.10.168
MA0122.10.658
MA0124.10.247
MA0125.10.186
MA0131.10.421
MA0135.10.283
MA0136.13.95279e-12
MA0137.20.258
MA0138.20.32
MA0139.10.851
MA0140.10.436
MA0141.10.156
MA0142.10.525
MA0143.10.929
MA0144.10.146
MA0145.10.716
MA0146.10.649
MA0147.10.112
MA0148.10.578
MA0149.10.201
MA0150.14.07598e-22
MA0152.11
MA0153.10.00318
MA0154.11.47969e-4
MA0155.10.863
MA0156.13.72868e-8
MA0157.10.915
MA0159.10.0407
MA0160.10.0384
MA0162.10.597
MA0163.12.01423e-7
MA0164.10.609
MA0258.10.0168
MA0259.10.882



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: CNhs13488

Novel motifP-value
10.117
100.018
1000.896
1010.828
1020.899
1030.331
1040.538
1050.0689
1060.00123
1070.389
1080.633
1090.431
110.225
1100.158
1110.0987
1120.373
1130.51
1140.0357
1150.197
1160.987
1170.0746
1180.228
1190.137
120.307
1200.944
1210.503
1220.563
1230.359
1240.616
1250.335
1260.27
1270.592
1280.0493
1290.471
130.0834
1300.245
1310.969
1320.0392
1330.67
1340.585
1350.932
1360.941
1370.0363
1380.373
1390.0824
140.549
1400.195
1410.306
1420.01
1430.0213
1440.626
1450.455
1460.817
1470.678
1480.0195
1490.885
150.198
1500.353
1510.528
1520.433
1530.615
1540.657
1550.989
1560.764
1570.403
1580.0179
1590.305
160.409
1600.434
1610.444
1620.189
1630.0932
1640.113
1650.326
1660.642
1670.147
1680.169
1690.0324
170.262
180.103
190.57
20.376
200.191
210.742
220.41
230.0667
240.445
250.498
260.075
270.448
280.436
290.259
30.182
300.428
310.773
320.373
330.285
340.844
350.106
360.0561
370.0767
380.359
390.911
40.837
400.181
410.0125
420.39
430.0254
440.5
450.852
460.229
470.678
480.591
490.12
50.338
500.972
510.588
520.458
530.623
540.503
550.613
560.683
570.839
580.199
590.333
60.836
600.0787
610.621
620.124
630.616
640.435
650.269
660.305
670.482
680.803
690.447
70.255
700.0819
710.0297
720.166
730.204
740.0485
750.153
760.104
770.707
780.116
790.602
80.415
800.251
810.354
820.306
830.00723
840.109
850.054
860.0474
870.655
880.786
890.311
90.483
900.163
910.316
920.37
930.414
940.0982
950.502
960.482
970.553
980.165
990.0271



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: CNhs13488


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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