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FF:11869-125B6: 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 B-glucan, 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
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 numberD3-10
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-Peripheral0.419
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-0.0658
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.604
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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-Whole0.23
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: CNhs13474

Jaspar motifP-value
MA0002.28.23847e-8
MA0003.10.366
MA0004.10.323
MA0006.10.946
MA0007.10.689
MA0009.10.224
MA0014.11
MA0017.10.0559
MA0018.20.12
MA0019.10.513
MA0024.10.00154
MA0025.10.00697
MA0027.10.848
MA0028.10.127
MA0029.10.244
MA0030.10.146
MA0031.10.322
MA0035.20.237
MA0038.10.102
MA0039.20.732
MA0040.10.456
MA0041.10.549
MA0042.10.71
MA0043.15.86409e-6
MA0046.10.0102
MA0047.20.604
MA0048.10.792
MA0050.13.39288e-5
MA0051.10.045
MA0052.10.0422
MA0055.10.951
MA0057.10.545
MA0058.10.143
MA0059.10.19
MA0060.14.04544e-11
MA0061.11.1148e-7
MA0062.20.642
MA0065.20.0101
MA0066.10.0244
MA0067.14.15791e-5
MA0068.10.199
MA0069.10.729
MA0070.10.0207
MA0071.10.304
MA0072.10.903
MA0073.10.416
MA0074.10.112
MA0076.10.103
MA0077.10.19
MA0078.10.436
MA0079.20.298
MA0080.22.66749e-14
MA0081.12.38443e-4
MA0083.10.77
MA0084.10.753
MA0087.10.966
MA0088.10.54
MA0090.10.224
MA0091.10.537
MA0092.10.287
MA0093.10.361
MA0099.24.73723e-41
MA0100.10.646
MA0101.11.23186e-7
MA0102.21.67667e-8
MA0103.10.365
MA0104.20.584
MA0105.17.57421e-11
MA0106.10.79
MA0107.13.0725e-9
MA0108.20.0647
MA0111.10.509
MA0112.25.05272e-5
MA0113.10.934
MA0114.10.154
MA0115.10.884
MA0116.13.64894e-4
MA0117.10.16
MA0119.10.246
MA0122.10.928
MA0124.10.572
MA0125.10.225
MA0131.10.45
MA0135.10.631
MA0136.14.6437e-15
MA0137.20.728
MA0138.20.897
MA0139.10.93
MA0140.10.153
MA0141.10.0887
MA0142.10.699
MA0143.10.825
MA0144.10.158
MA0145.10.258
MA0146.10.118
MA0147.10.679
MA0148.10.574
MA0149.10.18
MA0150.12.0963e-18
MA0152.10.787
MA0153.10.001
MA0154.10.00114
MA0155.10.685
MA0156.11.17605e-7
MA0157.10.879
MA0159.10.0194
MA0160.10.0419
MA0162.10.725
MA0163.14.19248e-8
MA0164.10.532
MA0258.10.00386
MA0259.10.674



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: CNhs13474

Novel motifP-value
10.118
100.0212
1000.899
1010.849
1020.726
1030.273
1040.562
1050.182
1065.28675e-4
1070.168
1080.935
1090.241
110.136
1100.24
1110.0283
1120.305
1130.517
1140.0107
1150.23
1160.786
1170.0415
1180.179
1190.123
120.311
1200.948
1210.623
1220.7
1230.0762
1240.544
1250.374
1260.171
1270.358
1280.0241
1290.447
130.154
1300.16
1310.76
1320.0719
1330.805
1340.495
1350.584
1360.934
1370.0121
1380.269
1390.0385
140.433
1400.117
1410.266
1420.0907
1430.0157
1440.564
1450.365
1460.545
1470.544
1480.00776
1490.651
150.169
1500.463
1510.333
1520.157
1530.514
1540.635
1550.619
1560.528
1570.368
1580.038
1590.473
160.319
1600.373
1610.521
1620.412
1630.14
1640.073
1650.196
1660.614
1670.219
1680.263
1690.00637
170.164
180.113
190.336
20.838
200.284
210.525
220.242
230.042
240.322
250.425
260.035
270.795
280.458
290.24
30.0916
300.49
310.714
320.933
330.334
340.547
350.116
360.124
370.0729
380.348
390.782
40.975
400.172
410.00682
420.378
430.0315
440.942
450.672
460.14
470.518
480.439
490.106
50.259
500.969
510.398
520.315
530.391
540.339
550.43
560.607
570.814
580.141
590.134
60.541
600.0447
610.636
620.0649
630.472
640.4
650.206
660.212
670.454
680.666
690.556
70.275
700.0219
710.0285
720.283
730.134
740.0798
750.0915
760.181
770.401
780.102
790.344
80.336
800.311
810.364
820.107
830.0518
840.233
850.0115
860.051
870.523
880.641
890.164
90.37
900.0615
910.313
920.219
930.579
940.0399
950.315
960.36
970.809
980.109
990.0996



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: CNhs13474


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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