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FF:11883-125D2: 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 - mock treated, 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 numberD5-4
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-Peripheral0.0943
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-0.122
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.293
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.39
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: CNhs13491

Jaspar motifP-value
MA0002.21.82801e-8
MA0003.10.293
MA0004.10.361
MA0006.10.741
MA0007.10.876
MA0009.10.406
MA0014.10.857
MA0017.10.0316
MA0018.20.315
MA0019.10.613
MA0024.14.76957e-4
MA0025.16.52506e-4
MA0027.10.775
MA0028.10.529
MA0029.10.59
MA0030.10.707
MA0031.10.495
MA0035.20.574
MA0038.10.02
MA0039.20.669
MA0040.10.155
MA0041.10.938
MA0042.10.441
MA0043.16.60022e-4
MA0046.10.0488
MA0047.20.258
MA0048.10.999
MA0050.12.66436e-6
MA0051.10.0189
MA0052.10.347
MA0055.10.476
MA0057.10.705
MA0058.10.171
MA0059.10.548
MA0060.11.59911e-10
MA0061.15.23069e-5
MA0062.20.00953
MA0065.20.0379
MA0066.10.154
MA0067.17.43953e-4
MA0068.10.879
MA0069.10.928
MA0070.10.0477
MA0071.10.253
MA0072.10.908
MA0073.10.251
MA0074.10.212
MA0076.10.669
MA0077.10.118
MA0078.10.435
MA0079.20.959
MA0080.21.02327e-16
MA0081.11.59772e-4
MA0083.10.99
MA0084.10.808
MA0087.10.474
MA0088.10.666
MA0090.10.0644
MA0091.10.573
MA0092.10.242
MA0093.10.364
MA0099.26.54659e-38
MA0100.10.648
MA0101.18.13684e-4
MA0102.22.61523e-9
MA0103.10.463
MA0104.20.957
MA0105.11.58618e-6
MA0106.10.505
MA0107.16.94001e-5
MA0108.20.0186
MA0111.10.346
MA0112.21.08717e-4
MA0113.10.914
MA0114.10.237
MA0115.10.815
MA0116.14.02943e-4
MA0117.10.284
MA0119.10.467
MA0122.10.734
MA0124.10.572
MA0125.10.307
MA0131.10.425
MA0135.10.243
MA0136.19.71207e-20
MA0137.20.492
MA0138.20.669
MA0139.10.635
MA0140.10.444
MA0141.10.0713
MA0142.10.877
MA0143.10.503
MA0144.10.158
MA0145.10.193
MA0146.10.028
MA0147.10.925
MA0148.10.931
MA0149.10.266
MA0150.11.43776e-12
MA0152.10.379
MA0153.10.0093
MA0154.10.00169
MA0155.10.67
MA0156.18.48451e-14
MA0157.10.257
MA0159.10.0301
MA0160.10.0212
MA0162.10.949
MA0163.14.2026e-5
MA0164.10.701
MA0258.10.00233
MA0259.10.436



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: CNhs13491

Novel motifP-value
10.156
100.0223
1000.668
1010.67
1020.396
1030.301
1040.541
1050.28
1066.99327e-4
1070.243
1080.992
1090.187
110.216
1100.369
1110.049
1120.27
1130.475
1140.0191
1150.214
1160.875
1170.0306
1180.216
1190.173
120.337
1200.675
1210.532
1220.675
1230.0411
1240.673
1250.816
1260.159
1270.228
1280.0162
1290.496
130.187
1300.26
1310.344
1320.0696
1330.79
1340.62
1350.253
1360.972
1370.00421
1380.165
1390.0475
140.414
1400.19
1410.333
1420.729
1430.0328
1440.86
1450.571
1460.441
1470.209
1480.0262
1490.742
150.157
1500.482
1510.273
1520.0799
1530.358
1540.611
1550.458
1560.826
1570.419
1580.106
1590.829
160.42
1600.607
1610.624
1620.244
1630.605
1640.129
1650.117
1660.359
1670.293
1680.396
1690.0106
170.205
180.25
190.267
20.896
200.441
210.349
220.154
230.0563
240.189
250.299
260.0526
270.715
280.44
290.397
30.0727
300.654
310.685
320.623
330.542
340.325
350.197
360.209
370.0565
380.311
390.811
40.618
400.18
410.0136
420.381
430.0437
440.914
450.661
460.172
470.537
480.466
490.109
50.216
500.955
510.342
520.29
530.225
540.321
550.398
560.628
570.933
580.104
590.108
60.596
600.0388
610.465
620.0357
630.493
640.525
650.211
660.348
670.461
680.878
690.838
70.227
700.0163
710.0346
720.241
730.0747
740.161
750.0558
760.28
770.413
780.0957
790.195
80.471
800.12
810.417
820.135
830.336
840.493
850.0127
860.0292
870.3
880.416
890.413
90.31
900.0705
910.343
920.188
930.161
940.036
950.376
960.433
970.926
980.167
990.114



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: CNhs13491


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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