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FF:11889-125D8: 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 17:35, 29 March 2012


Name:CD14+ monocytes - treated with B-glucan, 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 numberD5-10
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-Peripheral0.578
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-0.087
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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-Whole0.209
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: CNhs13495

Jaspar motifP-value
MA0002.27.01168e-8
MA0003.10.512
MA0004.10.0773
MA0006.10.745
MA0007.10.964
MA0009.10.354
MA0014.10.634
MA0017.10.119
MA0018.20.0111
MA0019.10.805
MA0024.10.00307
MA0025.16.19886e-5
MA0027.10.945
MA0028.10.209
MA0029.10.222
MA0030.10.384
MA0031.10.568
MA0035.20.31
MA0038.10.402
MA0039.20.83
MA0040.10.499
MA0041.10.975
MA0042.10.81
MA0043.12.7991e-9
MA0046.10.00914
MA0047.20.569
MA0048.10.599
MA0050.11.03217e-5
MA0051.10.0266
MA0052.17.97478e-4
MA0055.10.568
MA0057.10.477
MA0058.10.00937
MA0059.10.0541
MA0060.18.28291e-7
MA0061.19.88387e-10
MA0062.20.219
MA0065.20.0219
MA0066.10.0519
MA0067.11.99466e-7
MA0068.10.282
MA0069.10.65
MA0070.10.0691
MA0071.10.297
MA0072.10.699
MA0073.10.337
MA0074.10.145
MA0076.10.238
MA0077.10.208
MA0078.10.449
MA0079.20.276
MA0080.23.10476e-13
MA0081.12.34466e-4
MA0083.10.423
MA0084.10.592
MA0087.10.838
MA0088.10.441
MA0090.10.241
MA0091.10.791
MA0092.10.359
MA0093.10.0853
MA0099.22.09295e-45
MA0100.10.643
MA0101.11.67807e-10
MA0102.21.2896e-7
MA0103.10.195
MA0104.20.154
MA0105.12.81917e-13
MA0106.10.736
MA0107.12.58424e-12
MA0108.20.846
MA0111.10.574
MA0112.21.50921e-4
MA0113.10.991
MA0114.10.205
MA0115.10.707
MA0116.16.70031e-4
MA0117.10.0426
MA0119.10.255
MA0122.10.714
MA0124.10.328
MA0125.10.256
MA0131.10.492
MA0135.10.653
MA0136.11.98536e-15
MA0137.20.321
MA0138.20.368
MA0139.10.804
MA0140.10.313
MA0141.10.126
MA0142.10.546
MA0143.10.604
MA0144.10.136
MA0145.10.416
MA0146.10.172
MA0147.10.258
MA0148.10.629
MA0149.10.145
MA0150.11.13956e-22
MA0152.10.891
MA0153.10.00227
MA0154.18.93312e-4
MA0155.10.932
MA0156.13.28809e-9
MA0157.10.997
MA0159.10.0331
MA0160.10.024
MA0162.10.619
MA0163.11.18471e-6
MA0164.10.635
MA0258.10.0116
MA0259.10.99



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: CNhs13495

Novel motifP-value
10.129
100.0184
1000.785
1010.976
1020.769
1030.348
1040.487
1050.1
1067.06507e-4
1070.339
1080.888
1090.259
110.219
1100.228
1110.0544
1120.382
1130.486
1140.029
1150.146
1160.948
1170.0463
1180.208
1190.142
120.282
1200.973
1210.378
1220.623
1230.242
1240.495
1250.482
1260.182
1270.387
1280.0411
1290.434
130.0944
1300.167
1310.811
1320.0465
1330.958
1340.71
1350.942
1360.978
1370.00821
1380.286
1390.0434
140.518
1400.227
1410.271
1420.32
1430.0383
1440.698
1450.495
1460.449
1470.629
1480.0154
1490.967
150.174
1500.449
1510.428
1520.19
1530.694
1540.642
1550.808
1560.613
1570.313
1580.0105
1590.453
160.413
1600.492
1610.474
1620.191
1630.17
1640.0888
1650.202
1660.465
1670.218
1680.339
1690.0092
170.256
180.141
190.538
20.504
200.205
210.679
220.266
230.0617
240.354
250.382
260.0502
270.549
280.419
290.277
30.185
300.485
310.817
320.47
330.298
340.686
350.141
360.102
370.0625
380.349
390.857
40.983
400.133
410.00444
420.459
430.027
440.75
450.731
460.225
470.692
480.557
490.114
50.278
500.905
510.509
520.413
530.492
540.438
550.703
560.729
570.877
580.166
590.277
60.722
600.0639
610.683
620.0967
630.624
640.472
650.242
660.392
670.499
680.965
690.663
70.268
700.0586
710.0231
720.33
730.139
740.19
750.0869
760.141
770.613
780.116
790.844
80.459
800.218
810.421
820.227
830.00809
840.218
850.0182
860.0441
870.552
880.662
890.285
90.463
900.122
910.374
920.315
930.331
940.0575
950.402
960.419
970.747
980.15
990.0308



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: CNhs13495


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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