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FF:11868-125B5: 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 Candida, 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 numberD3-9
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-Peripheral1.055
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
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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-Whole0.228
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: CNhs13473

Jaspar motifP-value
MA0002.23.6418e-8
MA0003.10.98
MA0004.10.155
MA0006.10.818
MA0007.10.84
MA0009.10.497
MA0014.10.718
MA0017.10.249
MA0018.20.042
MA0019.10.548
MA0024.10.00303
MA0025.10.00121
MA0027.10.989
MA0028.10.0915
MA0029.10.142
MA0030.10.155
MA0031.10.326
MA0035.20.264
MA0038.10.608
MA0039.20.705
MA0040.10.724
MA0041.10.886
MA0042.10.439
MA0043.14.87361e-9
MA0046.10.00776
MA0047.20.264
MA0048.10.484
MA0050.13.8026e-11
MA0051.14.28228e-5
MA0052.10.00693
MA0055.10.33
MA0057.10.339
MA0058.10.0547
MA0059.10.0929
MA0060.16.66218e-8
MA0061.16.42839e-16
MA0062.20.798
MA0065.20.047
MA0066.10.0335
MA0067.16.24027e-7
MA0068.10.903
MA0069.10.796
MA0070.10.0202
MA0071.10.445
MA0072.10.602
MA0073.10.461
MA0074.10.114
MA0076.10.111
MA0077.10.282
MA0078.10.421
MA0079.20.113
MA0080.26.63657e-11
MA0081.15.97265e-4
MA0083.10.907
MA0084.10.656
MA0087.10.853
MA0088.10.482
MA0090.10.516
MA0091.10.708
MA0092.10.389
MA0093.10.203
MA0099.23.52211e-46
MA0100.10.822
MA0101.13.51463e-18
MA0102.21.40013e-9
MA0103.10.0583
MA0104.20.196
MA0105.16.77176e-21
MA0106.10.758
MA0107.11.16677e-21
MA0108.20.568
MA0111.10.472
MA0112.27.0498e-4
MA0113.10.971
MA0114.10.278
MA0115.10.639
MA0116.16.00074e-4
MA0117.10.0496
MA0119.10.156
MA0122.10.837
MA0124.10.488
MA0125.10.198
MA0131.10.467
MA0135.10.245
MA0136.17.74312e-12
MA0137.20.444
MA0138.20.322
MA0139.10.685
MA0140.10.379
MA0141.10.198
MA0142.10.802
MA0143.10.892
MA0144.10.177
MA0145.10.688
MA0146.10.654
MA0147.10.312
MA0148.10.575
MA0149.10.258
MA0150.16.79015e-21
MA0152.10.946
MA0153.10.00148
MA0154.12.51303e-4
MA0155.10.866
MA0156.19.71287e-8
MA0157.10.872
MA0159.10.0524
MA0160.10.0782
MA0162.10.901
MA0163.11.72668e-7
MA0164.10.653
MA0258.10.02
MA0259.10.968



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: CNhs13473

Novel motifP-value
10.113
100.0196
1000.976
1010.816
1020.997
1030.305
1040.478
1050.083
1067.66745e-4
1070.254
1080.626
1090.38
110.185
1100.154
1110.0633
1120.366
1130.466
1140.0265
1150.228
1160.99
1170.0626
1180.2
1190.195
120.353
1200.822
1210.574
1220.646
1230.274
1240.451
1250.284
1260.233
1270.588
1280.0478
1290.46
130.0756
1300.244
1310.818
1320.0616
1330.564
1340.525
1350.878
1360.96
1370.0414
1380.381
1390.0907
140.512
1400.277
1410.349
1420.0132
1430.0237
1440.591
1450.298
1460.851
1470.873
1480.00996
1490.866
150.167
1500.313
1510.471
1520.448
1530.537
1540.665
1550.919
1560.727
1570.506
1580.0391
1590.156
160.367
1600.401
1610.55
1620.231
1630.0772
1640.106
1650.317
1660.693
1670.213
1680.203
1690.0209
170.258
180.103
190.546
20.333
200.151
210.773
220.401
230.049
240.473
250.508
260.0782
270.382
280.414
290.22
30.142
300.381
310.758
320.402
330.189
340.863
350.0952
360.0526
370.0798
380.372
390.85
40.711
400.17
410.0129
420.359
430.0217
440.536
450.838
460.216
470.643
480.582
490.122
50.321
500.97
510.543
520.463
530.636
540.507
550.615
560.685
570.873
580.195
590.314
60.781
600.0643
610.702
620.115
630.552
640.446
650.237
660.245
670.46
680.718
690.355
70.264
700.0764
710.0285
720.149
730.223
740.0461
750.131
760.112
770.629
780.108
790.611
80.414
800.254
810.323
820.291
830.0118
840.0868
850.045
860.0768
870.575
880.781
890.311
90.421
900.131
910.4
920.427
930.637
940.099
950.377
960.367
970.528
980.107
990.0391



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: CNhs13473


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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