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FF:11880-125C8: 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 BCG, 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 numberD5-1
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-Peripheral0.721
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-0.158
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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-Whole0.289
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: CNhs13543

Jaspar motifP-value
MA0002.21.36583e-9
MA0003.10.639
MA0004.10.218
MA0006.10.663
MA0007.10.714
MA0009.10.79
MA0014.10.441
MA0017.10.108
MA0018.20.129
MA0019.10.82
MA0024.10.00806
MA0025.10.0019
MA0027.10.915
MA0028.10.443
MA0029.10.186
MA0030.10.263
MA0031.10.434
MA0035.20.27
MA0038.10.633
MA0039.20.932
MA0040.10.292
MA0041.10.545
MA0042.10.918
MA0043.17.25884e-8
MA0046.10.0228
MA0047.20.634
MA0048.10.652
MA0050.11.48174e-16
MA0051.11.24304e-10
MA0052.10.0359
MA0055.10.561
MA0057.10.575
MA0058.10.071
MA0059.10.0876
MA0060.17.81439e-8
MA0061.15.99181e-12
MA0062.20.12
MA0065.20.0123
MA0066.10.0347
MA0067.13.49943e-6
MA0068.10.872
MA0069.10.58
MA0070.10.00978
MA0071.10.407
MA0072.10.601
MA0073.10.395
MA0074.10.14
MA0076.10.505
MA0077.10.177
MA0078.10.481
MA0079.20.171
MA0080.25.52976e-12
MA0081.13.8826e-4
MA0083.10.422
MA0084.10.85
MA0087.10.76
MA0088.10.821
MA0090.10.49
MA0091.10.672
MA0092.10.303
MA0093.10.248
MA0099.23.96835e-42
MA0100.10.925
MA0101.15.19139e-13
MA0102.22.19192e-8
MA0103.10.0688
MA0104.20.19
MA0105.11.14841e-15
MA0106.10.959
MA0107.13.76824e-16
MA0108.20.383
MA0111.10.584
MA0112.29.32318e-5
MA0113.10.666
MA0114.10.174
MA0115.10.668
MA0116.14.28017e-4
MA0117.10.052
MA0119.10.162
MA0122.10.612
MA0124.10.486
MA0125.10.261
MA0131.10.494
MA0135.10.507
MA0136.15.2754e-14
MA0137.22.59538e-12
MA0138.20.317
MA0139.10.983
MA0140.10.329
MA0141.10.156
MA0142.10.724
MA0143.10.902
MA0144.11.61987e-5
MA0145.10.406
MA0146.10.41
MA0147.10.292
MA0148.10.982
MA0149.10.217
MA0150.18.75409e-22
MA0152.10.766
MA0153.10.00555
MA0154.15.34962e-4
MA0155.10.976
MA0156.11.02661e-10
MA0157.10.873
MA0159.10.0232
MA0160.10.0463
MA0162.10.932
MA0163.15.16864e-8
MA0164.10.713
MA0258.10.0112
MA0259.10.977



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: CNhs13543

Novel motifP-value
10.0893
100.0242
1000.987
1010.839
1020.928
1030.248
1040.526
1050.165
1060.00224
1070.318
1080.763
1090.245
110.162
1100.132
1110.0825
1120.351
1130.599
1140.0202
1150.19
1160.867
1170.0775
1180.209
1190.169
120.309
1200.33
1210.541
1220.554
1230.684
1240.85
1250.322
1260.25
1270.482
1280.0633
1290.383
130.0797
1300.348
1310.997
1320.0643
1330.611
1340.648
1350.494
1360.997
1370.0208
1380.277
1390.091
140.533
1400.564
1410.219
1420.098
1430.032
1440.619
1450.354
1460.9
1470.697
1480.0187
1490.997
150.145
1500.384
1510.482
1520.4
1530.889
1540.776
1550.808
1560.512
1570.815
1580.0853
1590.114
160.299
1600.396
1610.464
1620.217
1630.136
1640.15
1650.224
1660.745
1670.236
1680.126
1690.00949
170.267
180.145
190.438
20.528
200.23
210.705
220.298
230.0448
240.314
250.361
260.0762
270.68
280.44
290.234
30.146
300.483
310.804
320.528
330.206
340.741
350.147
360.0668
370.0695
380.387
390.842
40.877
400.201
410.0174
420.347
430.0273
440.776
450.835
460.19
470.543
480.476
490.173
50.254
500.927
510.491
520.461
530.642
540.432
550.616
560.705
570.877
580.171
590.306
60.83
600.0547
610.732
620.0778
630.548
640.42
650.259
660.31
670.484
680.861
690.343
70.218
700.0461
710.0318
720.2
730.204
740.0719
750.127
760.176
770.557
780.152
790.986
80.405
800.149
810.375
820.249
830.0153
840.321
850.0479
860.0729
870.417
880.672
890.175
90.376
900.0971
910.315
920.303
930.354
940.0858
950.379
960.591
970.636
980.109
990.0602



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: CNhs13543


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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