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FF:11879-125C7: 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 B-glucan, 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 numberD4-10
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-Peripheral0.422
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-0.0562
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.485
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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-Whole0.15
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: CNhs13489

Jaspar motifP-value
MA0002.23.07849e-6
MA0003.10.46
MA0004.10.14
MA0006.10.856
MA0007.10.775
MA0009.10.246
MA0014.10.911
MA0017.10.0816
MA0018.20.0315
MA0019.10.709
MA0024.10.00202
MA0025.10.00953
MA0027.10.881
MA0028.10.0628
MA0029.10.339
MA0030.10.2
MA0031.10.398
MA0035.20.281
MA0038.10.146
MA0039.20.79
MA0040.10.626
MA0041.10.278
MA0042.10.326
MA0043.13.69393e-6
MA0046.10.0109
MA0047.20.61
MA0048.10.814
MA0050.12.75947e-4
MA0051.10.13
MA0052.10.00128
MA0055.10.92
MA0057.10.445
MA0058.10.0275
MA0059.10.116
MA0060.12.5311e-9
MA0061.18.04001e-8
MA0062.20.763
MA0065.20.0155
MA0066.10.0666
MA0067.12.61233e-6
MA0068.10.157
MA0069.10.736
MA0070.10.0228
MA0071.10.291
MA0072.10.98
MA0073.10.438
MA0074.10.186
MA0076.10.0611
MA0077.10.221
MA0078.10.557
MA0079.20.328
MA0080.26.38771e-14
MA0081.14.06515e-4
MA0083.10.711
MA0084.10.408
MA0087.10.718
MA0088.10.333
MA0090.10.222
MA0091.10.489
MA0092.10.337
MA0093.10.146
MA0099.29.54845e-44
MA0100.10.47
MA0101.13.93478e-7
MA0102.25.49247e-7
MA0103.10.342
MA0104.20.262
MA0105.13.2548e-11
MA0106.10.979
MA0107.11.26037e-8
MA0108.20.341
MA0111.10.501
MA0112.26.33189e-5
MA0113.10.978
MA0114.10.189
MA0115.10.606
MA0116.15.02966e-4
MA0117.10.0684
MA0119.10.428
MA0122.10.81
MA0124.10.393
MA0125.10.303
MA0131.10.385
MA0135.10.81
MA0136.18.62818e-15
MA0137.20.465
MA0138.20.557
MA0139.10.806
MA0140.10.267
MA0141.10.12
MA0142.10.402
MA0143.10.623
MA0144.10.142
MA0145.10.378
MA0146.10.141
MA0147.10.387
MA0148.10.498
MA0149.10.151
MA0150.12.7555e-22
MA0152.10.855
MA0153.10.00485
MA0154.10.00165
MA0155.10.943
MA0156.13.45434e-7
MA0157.10.924
MA0159.10.0196
MA0160.10.0255
MA0162.10.705
MA0163.13.53616e-7
MA0164.10.562
MA0258.10.00506
MA0259.10.759



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: CNhs13489

Novel motifP-value
10.101
100.0212
1000.773
1010.871
1020.604
1030.386
1040.604
1050.145
1063.19758e-4
1070.244
1080.969
1090.315
110.191
1100.255
1110.0358
1120.319
1130.421
1140.0193
1150.25
1160.944
1170.0667
1180.193
1190.106
120.352
1200.682
1210.474
1220.644
1230.0871
1240.455
1250.436
1260.284
1270.458
1280.031
1290.507
130.153
1300.128
1310.805
1320.0547
1330.704
1340.726
1350.759
1360.984
1370.0138
1380.289
1390.0337
140.511
1400.159
1410.346
1420.2
1430.0304
1440.602
1450.521
1460.479
1470.462
1480.0112
1490.81
150.159
1500.465
1510.384
1520.122
1530.416
1540.495
1550.671
1560.577
1570.293
1580.0132
1590.818
160.352
1600.428
1610.549
1620.248
1630.144
1640.0971
1650.23
1660.466
1670.142
1680.365
1690.0091
170.224
180.119
190.424
20.813
200.261
210.432
220.233
230.0473
240.342
250.413
260.054
270.718
280.434
290.359
30.139
300.495
310.779
320.721
330.475
340.583
350.163
360.161
370.0606
380.377
390.796
40.938
400.182
410.00974
420.428
430.0287
440.941
450.679
460.18
470.638
480.589
490.0994
50.314
500.945
510.463
520.33
530.383
540.39
550.553
560.685
570.77
580.144
590.188
60.657
600.0539
610.642
620.0732
630.534
640.414
650.217
660.301
670.56
680.827
690.831
70.294
700.0283
710.0335
720.287
730.109
740.227
750.12
760.163
770.507
780.0835
790.559
80.44
800.327
810.354
820.157
830.0245
840.205
850.011
860.0305
870.633
880.657
890.249
90.435
900.111
910.256
920.187
930.277
940.0556
950.457
960.361
970.799
980.126
990.0565



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: CNhs13489


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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