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FF:11862-125A8: Difference between revisions

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|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:32, 29 March 2012


Name:CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor1
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
sexfemale
age69
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD3-3
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-Peripheral0.479
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-penis0.00974
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
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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-Whole0.244
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: CNhs13467

Jaspar motifP-value
MA0002.21.50802e-6
MA0003.10.787
MA0004.10.171
MA0006.10.629
MA0007.10.705
MA0009.10.228
MA0014.10.901
MA0017.10.119
MA0018.20.0726
MA0019.10.526
MA0024.18.07187e-4
MA0025.10.0232
MA0027.10.774
MA0028.10.143
MA0029.10.104
MA0030.10.0652
MA0031.10.359
MA0035.20.135
MA0038.10.126
MA0039.20.808
MA0040.10.519
MA0041.10.111
MA0042.10.281
MA0043.11.06923e-6
MA0046.10.012
MA0047.20.638
MA0048.10.557
MA0050.12.02491e-20
MA0051.16.88155e-12
MA0052.10.0519
MA0055.10.664
MA0057.10.569
MA0058.10.0551
MA0059.10.138
MA0060.12.43199e-9
MA0061.12.90346e-6
MA0062.20.459
MA0065.20.0195
MA0066.10.0718
MA0067.11.52463e-6
MA0068.10.373
MA0069.10.585
MA0070.10.0118
MA0071.10.406
MA0072.10.972
MA0073.10.555
MA0074.10.138
MA0076.10.149
MA0077.10.161
MA0078.10.439
MA0079.20.223
MA0080.21.10366e-12
MA0081.12.86209e-4
MA0083.10.452
MA0084.10.946
MA0087.10.803
MA0088.10.453
MA0090.10.34
MA0091.10.584
MA0092.10.352
MA0093.10.214
MA0099.24.10853e-43
MA0100.10.716
MA0101.13.25159e-5
MA0102.26.46309e-7
MA0103.10.267
MA0104.20.359
MA0105.12.90705e-10
MA0106.10.984
MA0107.15.61104e-6
MA0108.20.147
MA0111.10.609
MA0112.22.02908e-4
MA0113.10.631
MA0114.10.278
MA0115.10.847
MA0116.14.06752e-4
MA0117.10.0716
MA0119.10.185
MA0122.10.958
MA0124.10.72
MA0125.10.261
MA0131.10.571
MA0135.10.35
MA0136.12.33104e-13
MA0137.21.06974e-10
MA0138.20.542
MA0139.10.895
MA0140.10.139
MA0141.10.131
MA0142.10.844
MA0143.10.897
MA0144.14.24584e-5
MA0145.10.504
MA0146.10.202
MA0147.10.493
MA0148.10.641
MA0149.10.276
MA0150.11.6167e-20
MA0152.10.659
MA0153.10.00236
MA0154.10.00257
MA0155.10.955
MA0156.11.10842e-8
MA0157.10.971
MA0159.10.0192
MA0160.10.0332
MA0162.10.683
MA0163.11.18406e-7
MA0164.10.539
MA0258.10.00618
MA0259.10.996



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: CNhs13467

Novel motifP-value
10.0898
100.0129
1000.934
1010.988
1020.822
1030.401
1040.604
1050.204
1069.23421e-4
1070.27
1080.938
1090.294
110.15
1100.121
1110.0256
1120.376
1130.523
1140.0134
1150.288
1160.821
1170.0385
1180.168
1190.137
120.349
1200.968
1210.501
1220.736
1230.0807
1240.637
1250.358
1260.292
1270.421
1280.039
1290.492
130.0767
1300.0724
1310.768
1320.0765
1330.569
1340.596
1350.746
1360.887
1370.0152
1380.223
1390.0543
140.421
1400.316
1410.271
1420.0982
1430.0457
1440.812
1450.269
1460.547
1470.516
1480.0176
1490.823
150.177
1500.438
1510.418
1520.216
1530.734
1540.435
1550.719
1560.499
1570.53
1580.0165
1590.929
160.294
1600.408
1610.605
1620.223
1630.124
1640.0727
1650.179
1660.633
1670.104
1680.346
1690.0117
170.229
180.175
190.428
20.507
200.157
210.512
220.365
230.0437
240.321
250.421
260.0476
270.536
280.48
290.212
30.101
300.393
310.888
320.929
330.284
340.786
350.151
360.0885
370.0724
380.407
390.863
40.812
400.207
410.0123
420.366
430.032
440.941
450.965
460.184
470.539
480.526
490.123
50.327
500.976
510.523
520.398
530.465
540.404
550.551
560.711
570.742
580.138
590.355
60.674
600.0518
610.704
620.0728
630.482
640.397
650.26
660.24
670.619
680.803
690.462
70.295
700.0343
710.0305
720.217
730.166
740.0896
750.093
760.133
770.57
780.0784
790.2
80.394
800.381
810.377
820.173
830.0697
840.246
850.0191
860.0677
870.98
880.578
890.327
90.531
900.0665
910.255
920.26
930.445
940.0684
950.348
960.666
970.792
980.135
990.0406



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: CNhs13467


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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