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FF:11882-125D1: 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 17:37, 29 March 2012


Name:CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor3
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
age21
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD5-3
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-Peripheral0.606
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-0.151
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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-Whole0.319
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: CNhs13544

Jaspar motifP-value
MA0002.26.60303e-10
MA0003.10.622
MA0004.10.111
MA0006.10.634
MA0007.10.839
MA0009.10.594
MA0014.10.453
MA0017.10.0978
MA0018.20.0378
MA0019.10.95
MA0024.10.00368
MA0025.16.34924e-4
MA0027.10.806
MA0028.10.456
MA0029.10.174
MA0030.10.444
MA0031.10.63
MA0035.20.247
MA0038.10.582
MA0039.20.63
MA0040.10.186
MA0041.10.619
MA0042.10.913
MA0043.13.64922e-8
MA0046.10.029
MA0047.20.777
MA0048.10.733
MA0050.11.71127e-16
MA0051.14.40764e-10
MA0052.10.0144
MA0055.10.633
MA0057.10.575
MA0058.10.0171
MA0059.10.0647
MA0060.11.26747e-6
MA0061.17.29259e-9
MA0062.20.058
MA0065.20.0114
MA0066.10.0307
MA0067.12.29024e-7
MA0068.10.763
MA0069.10.493
MA0070.10.0271
MA0071.10.44
MA0072.10.71
MA0073.10.376
MA0074.10.156
MA0076.10.524
MA0077.10.139
MA0078.10.492
MA0079.20.251
MA0080.21.53982e-12
MA0081.12.81828e-4
MA0083.10.347
MA0084.10.794
MA0087.10.99
MA0088.10.747
MA0090.10.33
MA0091.10.733
MA0092.10.334
MA0093.10.128
MA0099.24.07564e-45
MA0100.10.974
MA0101.12.32834e-8
MA0102.29.63961e-8
MA0103.10.0983
MA0104.20.132
MA0105.11.66105e-12
MA0106.10.773
MA0107.16.87709e-10
MA0108.20.47
MA0111.10.666
MA0112.28.98939e-5
MA0113.10.708
MA0114.10.223
MA0115.10.562
MA0116.14.73235e-4
MA0117.10.0286
MA0119.10.236
MA0122.10.712
MA0124.10.416
MA0125.10.31
MA0131.10.545
MA0135.10.612
MA0136.15.41319e-15
MA0137.21.24682e-13
MA0138.20.293
MA0139.10.964
MA0140.10.242
MA0141.10.14
MA0142.10.8
MA0143.10.989
MA0144.17.55928e-6
MA0145.10.451
MA0146.10.327
MA0147.10.253
MA0148.10.992
MA0149.10.262
MA0150.18.12196e-23
MA0152.10.736
MA0153.10.00696
MA0154.10.00128
MA0155.10.952
MA0156.11.50628e-11
MA0157.10.78
MA0159.10.0228
MA0160.10.0237
MA0162.10.7
MA0163.14.97154e-7
MA0164.10.694
MA0258.10.00894
MA0259.10.876



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: CNhs13544

Novel motifP-value
10.0925
100.0203
1000.903
1010.753
1020.96
1030.345
1040.53
1050.152
1060.0016
1070.381
1080.7
1090.225
110.199
1100.131
1110.073
1120.363
1130.591
1140.0244
1150.197
1160.927
1170.0687
1180.204
1190.181
120.293
1200.481
1210.408
1220.546
1230.518
1240.868
1250.47
1260.213
1270.42
1280.0609
1290.458
130.0766
1300.268
1310.988
1320.0496
1330.803
1340.734
1350.522
1360.993
1370.013
1380.306
1390.0861
140.491
1400.498
1410.26
1420.0663
1430.0323
1440.724
1450.414
1460.737
1470.512
1480.0261
1490.884
150.161
1500.419
1510.381
1520.292
1530.899
1540.609
1550.816
1560.39
1570.753
1580.0364
1590.168
160.358
1600.511
1610.527
1620.159
1630.161
1640.15
1650.195
1660.523
1670.156
1680.165
1690.0121
170.324
180.187
190.491
20.511
200.243
210.655
220.287
230.0597
240.293
250.329
260.0716
270.651
280.448
290.192
30.194
300.509
310.821
320.507
330.232
340.716
350.198
360.0808
370.0699
380.443
390.971
40.845
400.206
410.0121
420.429
430.0314
440.769
450.87
460.212
470.609
480.535
490.171
50.267
500.891
510.503
520.481
530.605
540.427
550.71
560.764
570.946
580.163
590.375
60.837
600.0696
610.782
620.0796
630.647
640.434
650.298
660.373
670.56
680.937
690.452
70.245
700.0538
710.0307
720.171
730.168
740.0875
750.116
760.229
770.697
780.114
790.733
80.504
800.151
810.408
820.29
830.00571
840.42
850.0405
860.0582
870.493
880.587
890.232
90.452
900.101
910.312
920.317
930.244
940.0739
950.337
960.619
970.714
980.194
990.0282



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: CNhs13544


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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