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FF:11887-125D6: 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 17:37, 29 March 2012


Name:CD14+ monocytes - treated with Cryptococcus, 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 numberD5-8
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-Peripheral0.41
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-0.152
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.371
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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-Whole0.279
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: CNhs13546

Jaspar motifP-value
MA0002.22.65716e-9
MA0003.10.367
MA0004.10.293
MA0006.10.986
MA0007.10.807
MA0009.10.715
MA0014.10.561
MA0017.10.0534
MA0018.20.0317
MA0019.10.988
MA0024.10.00179
MA0025.11.82378e-4
MA0027.10.818
MA0028.10.664
MA0029.10.276
MA0030.10.609
MA0031.10.775
MA0035.20.364
MA0038.10.377
MA0039.20.812
MA0040.10.219
MA0041.10.426
MA0042.10.572
MA0043.13.73339e-7
MA0046.10.0226
MA0047.20.914
MA0048.10.97
MA0050.11.38239e-4
MA0051.10.0643
MA0052.10.0335
MA0055.10.894
MA0057.10.578
MA0058.10.0899
MA0059.10.166
MA0060.11.12531e-8
MA0061.17.42852e-8
MA0062.20.0526
MA0065.20.00746
MA0066.10.0263
MA0067.11.12029e-5
MA0068.10.873
MA0069.10.761
MA0070.10.0245
MA0071.10.26
MA0072.10.606
MA0073.10.242
MA0074.10.198
MA0076.10.677
MA0077.10.108
MA0078.10.468
MA0079.20.265
MA0080.23.98268e-14
MA0081.11.93025e-4
MA0083.10.645
MA0084.10.775
MA0087.10.75
MA0088.10.846
MA0090.10.237
MA0091.10.672
MA0092.10.286
MA0093.10.289
MA0099.21.04062e-41
MA0100.10.853
MA0101.11.15574e-7
MA0102.23.36993e-8
MA0103.10.143
MA0104.20.449
MA0105.11.95931e-11
MA0106.10.816
MA0107.19.60169e-10
MA0108.20.335
MA0111.10.471
MA0112.23.64364e-5
MA0113.10.75
MA0114.10.138
MA0115.10.85
MA0116.12.48927e-4
MA0117.10.0682
MA0119.10.31
MA0122.10.658
MA0124.10.41
MA0125.10.275
MA0131.10.509
MA0135.10.935
MA0136.13.26574e-17
MA0137.20.135
MA0138.20.711
MA0139.10.997
MA0140.10.37
MA0141.10.0881
MA0142.10.451
MA0143.10.638
MA0144.10.0894
MA0145.10.33
MA0146.10.21
MA0147.10.558
MA0148.10.991
MA0149.10.149
MA0150.13.12296e-19
MA0152.10.983
MA0153.10.00326
MA0154.17.11656e-4
MA0155.10.745
MA0156.19.31238e-11
MA0157.10.687
MA0159.10.00624
MA0160.10.0283
MA0162.10.859
MA0163.11.15909e-7
MA0164.10.703
MA0258.10.0054
MA0259.10.759



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: CNhs13546

Novel motifP-value
10.0877
100.021
1000.761
1010.971
1020.786
1030.229
1040.577
1050.185
1060.00216
1070.321
1080.762
1090.194
110.145
1100.201
1110.0638
1120.316
1130.554
1140.0196
1150.122
1160.85
1170.0577
1180.184
1190.148
120.304
1200.361
1210.472
1220.588
1230.44
1240.715
1250.428
1260.172
1270.362
1280.0445
1290.373
130.127
1300.378
1310.691
1320.0603
1330.964
1340.539
1350.305
1360.89
1370.00743
1380.347
1390.0474
140.583
1400.216
1410.309
1420.516
1430.0164
1440.622
1450.535
1460.606
1470.524
1480.0185
1490.837
150.14
1500.496
1510.425
1520.241
1530.504
1540.76
1550.706
1560.517
1570.562
1580.0562
1590.116
160.317
1600.523
1610.47
1620.226
1630.25
1640.151
1650.164
1660.584
1670.23
1680.15
1690.00779
170.242
180.123
190.342
20.744
200.318
210.614
220.231
230.0647
240.304
250.308
260.0504
270.856
280.388
290.272
30.143
300.523
310.79
320.618
330.282
340.579
350.137
360.0987
370.0634
380.365
390.789
40.817
400.202
410.0104
420.371
430.0321
440.934
450.7
460.164
470.477
480.464
490.126
50.236
500.913
510.412
520.373
530.453
540.356
550.63
560.712
570.928
580.125
590.178
60.619
600.0512
610.571
620.0532
630.566
640.437
650.233
660.41
670.395
680.553
690.633
70.22
700.0325
710.0218
720.257
730.148
740.0721
750.0884
760.204
770.483
780.131
790.764
80.4
800.101
810.34
820.141
830.0612
840.401
850.0221
860.058
870.294
880.628
890.166
90.366
900.085
910.362
920.208
930.173
940.0465
950.369
960.392
970.786
980.149
990.0743



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: CNhs13546


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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