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FF:11870-125B7: 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 17:33, 29 March 2012


Name:CD14+ monocytes - treated with BCG, 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 numberD4-1
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-Peripheral0.552
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-0.0631
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.661
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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-Whole0.248
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: CNhs13475

Jaspar motifP-value
MA0002.26.93552e-8
MA0003.10.558
MA0004.10.331
MA0006.10.696
MA0007.10.627
MA0009.10.363
MA0014.10.904
MA0017.10.0833
MA0018.20.171
MA0019.10.657
MA0024.10.00242
MA0025.10.0101
MA0027.10.821
MA0028.10.14
MA0029.10.227
MA0030.10.127
MA0031.10.286
MA0035.20.206
MA0038.10.211
MA0039.20.687
MA0040.10.329
MA0041.10.87
MA0042.10.461
MA0043.12.81541e-6
MA0046.10.0287
MA0047.20.714
MA0048.10.703
MA0050.12.46403e-19
MA0051.11.44873e-11
MA0052.10.037
MA0055.10.792
MA0057.10.616
MA0058.10.136
MA0059.10.208
MA0060.11.33644e-9
MA0061.13.4108e-9
MA0062.20.521
MA0065.20.0122
MA0066.10.0373
MA0067.13.29975e-6
MA0068.10.234
MA0069.10.639
MA0070.10.0194
MA0071.10.363
MA0072.10.789
MA0073.10.477
MA0074.10.154
MA0076.10.17
MA0077.10.225
MA0078.10.484
MA0079.20.224
MA0080.21.12398e-12
MA0081.15.41148e-4
MA0083.10.507
MA0084.10.754
MA0087.10.995
MA0088.10.647
MA0090.10.423
MA0091.10.573
MA0092.10.261
MA0093.10.381
MA0099.21.02084e-43
MA0100.10.718
MA0101.12.86246e-9
MA0102.23.3324e-8
MA0103.10.172
MA0104.20.382
MA0105.11.29928e-12
MA0106.10.996
MA0107.13.60182e-11
MA0108.20.198
MA0111.10.611
MA0112.24.81062e-5
MA0113.10.702
MA0114.10.2
MA0115.10.845
MA0116.13.32092e-4
MA0117.10.0814
MA0119.10.221
MA0122.10.721
MA0124.10.522
MA0125.10.286
MA0131.10.345
MA0135.10.466
MA0136.14.69495e-13
MA0137.24.66212e-12
MA0138.20.513
MA0139.10.827
MA0140.10.23
MA0141.10.127
MA0142.10.507
MA0143.10.967
MA0144.11.89902e-5
MA0145.10.322
MA0146.10.284
MA0147.10.501
MA0148.10.819
MA0149.10.188
MA0150.11.73344e-21
MA0152.10.791
MA0153.10.00345
MA0154.10.00104
MA0155.10.901
MA0156.11.24001e-8
MA0157.10.999
MA0159.10.0234
MA0160.10.038
MA0162.10.931
MA0163.11.70711e-8
MA0164.10.577
MA0258.10.00427
MA0259.10.818



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: CNhs13475

Novel motifP-value
10.0831
100.0227
1000.989
1010.816
1020.803
1030.274
1040.533
1050.152
1067.61515e-4
1070.21
1080.87
1090.248
110.164
1100.138
1110.0371
1120.38
1130.561
1140.0171
1150.231
1160.873
1170.0723
1180.203
1190.141
120.347
1200.783
1210.524
1220.556
1230.218
1240.795
1250.387
1260.267
1270.439
1280.0377
1290.41
130.108
1300.17
1310.771
1320.0624
1330.563
1340.689
1350.633
1360.917
1370.0313
1380.213
1390.0627
140.439
1400.332
1410.226
1420.0571
1430.0239
1440.655
1450.294
1460.752
1470.595
1480.013
1490.876
150.166
1500.416
1510.392
1520.243
1530.819
1540.504
1550.911
1560.499
1570.613
1580.0386
1590.504
160.3
1600.361
1610.456
1620.21
1630.0778
1640.114
1650.137
1660.691
1670.147
1680.219
1690.00733
170.192
180.125
190.453
20.657
200.26
210.567
220.31
230.04
240.322
250.409
260.066
270.762
280.487
290.254
30.11
300.539
310.789
320.803
330.284
340.646
350.183
360.0816
370.0714
380.394
390.813
40.921
400.223
410.016
420.369
430.0308
440.898
450.791
460.183
470.528
480.476
490.133
50.286
500.994
510.419
520.377
530.497
540.371
550.403
560.675
570.778
580.145
590.218
60.877
600.0463
610.672
620.0754
630.488
640.439
650.229
660.281
670.547
680.867
690.449
70.265
700.0381
710.0379
720.164
730.171
740.11
750.131
760.192
770.511
780.111
790.401
80.357
800.215
810.331
820.189
830.0255
840.226
850.0206
860.052
870.658
880.619
890.233
90.362
900.0926
910.296
920.273
930.387
940.0802
950.363
960.45
970.66
980.101
990.0761



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: CNhs13475


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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