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FF:11881-125C9: 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 IFN + N-hexane, 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 numberD5-2
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-Peripheral0.154
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-0.1
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.543
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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-Whole0.268
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: CNhs13490

Jaspar motifP-value
MA0002.22.50005e-8
MA0003.10.317
MA0004.10.551
MA0006.10.953
MA0007.10.735
MA0009.10.373
MA0014.10.649
MA0017.10.0229
MA0018.20.487
MA0019.10.738
MA0024.10.00162
MA0025.10.022
MA0027.10.93
MA0028.10.154
MA0029.10.296
MA0030.10.445
MA0031.10.837
MA0035.20.341
MA0038.10.047
MA0039.20.994
MA0040.10.107
MA0041.10.98
MA0042.10.806
MA0043.10.00112
MA0046.10.174
MA0047.20.592
MA0048.10.965
MA0050.18.46872e-25
MA0051.15.2167e-16
MA0052.10.451
MA0055.10.508
MA0057.10.901
MA0058.10.35
MA0059.10.492
MA0060.12.46421e-11
MA0061.12.7522e-6
MA0062.20.344
MA0065.20.00727
MA0066.10.0784
MA0067.12.55508e-4
MA0068.10.581
MA0069.10.527
MA0070.10.00211
MA0071.10.396
MA0072.10.834
MA0073.10.391
MA0074.10.256
MA0076.10.185
MA0077.10.171
MA0078.10.503
MA0079.20.617
MA0080.27.8663e-15
MA0081.12.55599e-4
MA0083.10.479
MA0084.10.914
MA0087.10.855
MA0088.10.558
MA0090.10.122
MA0091.10.466
MA0092.10.186
MA0093.10.622
MA0099.22.63568e-32
MA0100.10.778
MA0101.14.83733e-5
MA0102.29.51198e-9
MA0103.10.39
MA0104.20.981
MA0105.12.44481e-8
MA0106.10.741
MA0107.11.64107e-6
MA0108.20.0323
MA0111.10.455
MA0112.28.34784e-5
MA0113.10.538
MA0114.10.158
MA0115.10.839
MA0116.12.66716e-4
MA0117.10.224
MA0119.10.358
MA0122.10.684
MA0124.10.872
MA0125.10.442
MA0131.10.351
MA0135.10.981
MA0136.14.49022e-15
MA0137.21.02123e-18
MA0138.20.888
MA0139.10.917
MA0140.10.278
MA0141.10.0885
MA0142.10.577
MA0143.10.59
MA0144.13.47101e-7
MA0145.10.229
MA0146.10.0821
MA0147.10.941
MA0148.10.77
MA0149.10.299
MA0150.12.27683e-14
MA0152.10.94
MA0153.10.0345
MA0154.10.00232
MA0155.10.829
MA0156.15.55096e-10
MA0157.10.507
MA0159.10.0169
MA0160.10.0279
MA0162.10.944
MA0163.11.05913e-6
MA0164.10.83
MA0258.10.00209
MA0259.10.543



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: CNhs13490

Novel motifP-value
10.112
100.0238
1000.813
1010.845
1020.586
1030.244
1040.622
1050.269
1063.16887e-4
1070.218
1080.992
1090.191
110.14
1100.177
1110.0717
1120.327
1130.53
1140.00884
1150.18
1160.865
1170.0808
1180.22
1190.153
120.415
1200.477
1210.586
1220.552
1230.196
1240.792
1250.507
1260.297
1270.31
1280.0324
1290.426
130.171
1300.143
1310.411
1320.113
1330.908
1340.469
1350.406
1360.913
1370.0135
1380.134
1390.0663
140.442
1400.311
1410.192
1420.298
1430.0432
1440.797
1450.504
1460.702
1470.417
1480.0127
1490.768
150.144
1500.453
1510.256
1520.0973
1530.664
1540.479
1550.747
1560.53
1570.61
1580.0981
1590.808
160.34
1600.46
1610.499
1620.308
1630.287
1640.207
1650.0618
1660.63
1670.291
1680.223
1690.00743
170.23
180.178
190.265
20.92
200.389
210.396
220.197
230.031
240.224
250.354
260.0649
270.805
280.476
290.304
30.084
300.617
310.846
320.8
330.347
340.497
350.192
360.134
370.0687
380.467
390.786
40.894
400.247
410.0499
420.356
430.0392
440.655
450.771
460.162
470.449
480.42
490.123
50.175
500.95
510.343
520.245
530.352
540.283
550.358
560.685
570.844
580.11
590.183
60.716
600.0249
610.65
620.0354
630.442
640.489
650.237
660.267
670.478
680.825
690.605
70.304
700.0187
710.0517
720.115
730.105
740.125
750.114
760.382
770.401
780.105
790.0563
80.387
800.147
810.328
820.105
830.394
840.43
850.0171
860.0357
870.496
880.529
890.294
90.275
900.0783
910.333
920.175
930.176
940.049
950.455
960.318
970.768
980.075
990.122



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: CNhs13490


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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