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FF:11875-125C3: 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 17:36, 29 March 2012


Name:CD14+ monocytes - treated with lipopolysaccharide, donor2
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 numberD4-6
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-Peripheral0.861
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
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C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
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-Whole0.136
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: CNhs13533

Jaspar motifP-value
MA0002.21.53917e-7
MA0003.10.63
MA0004.10.335
MA0006.10.908
MA0007.10.974
MA0009.10.469
MA0014.10.867
MA0017.10.223
MA0018.20.129
MA0019.10.54
MA0024.10.00592
MA0025.10.00155
MA0027.10.962
MA0028.10.13
MA0029.10.135
MA0030.10.118
MA0031.10.301
MA0035.20.309
MA0038.10.601
MA0039.20.867
MA0040.10.746
MA0041.10.417
MA0042.10.936
MA0043.19.80958e-9
MA0046.10.0227
MA0047.20.334
MA0048.10.689
MA0050.13.31653e-15
MA0051.11.42645e-9
MA0052.10.173
MA0055.10.508
MA0057.10.398
MA0058.10.152
MA0059.10.182
MA0060.12.44784e-7
MA0061.18.97438e-21
MA0062.20.576
MA0065.20.0289
MA0066.10.052
MA0067.16.21139e-6
MA0068.10.534
MA0069.10.771
MA0070.10.0237
MA0071.10.552
MA0072.10.621
MA0073.10.441
MA0074.10.2
MA0076.10.147
MA0077.10.332
MA0078.10.555
MA0079.20.188
MA0080.21.05452e-11
MA0081.14.76743e-4
MA0083.10.518
MA0084.10.521
MA0087.10.636
MA0088.10.588
MA0090.10.477
MA0091.10.898
MA0092.10.391
MA0093.10.361
MA0099.22.73311e-45
MA0100.10.757
MA0101.11.09862e-23
MA0102.21.0476e-9
MA0103.10.0343
MA0104.20.292
MA0105.11.37784e-23
MA0106.10.962
MA0107.13.05257e-30
MA0108.20.705
MA0111.10.549
MA0112.24.9562e-4
MA0113.10.799
MA0114.10.209
MA0115.10.704
MA0116.11.68758e-4
MA0117.10.0528
MA0119.10.154
MA0122.10.599
MA0124.10.244
MA0125.10.272
MA0131.10.451
MA0135.10.386
MA0136.19.77454e-13
MA0137.20.0225
MA0138.20.138
MA0139.10.795
MA0140.10.477
MA0141.10.288
MA0142.10.498
MA0143.10.989
MA0144.10.0308
MA0145.10.526
MA0146.10.725
MA0147.10.403
MA0148.10.731
MA0149.10.204
MA0150.11.90623e-24
MA0152.10.796
MA0153.10.00306
MA0154.11.24213e-4
MA0155.10.896
MA0156.13.06626e-9
MA0157.10.995
MA0159.10.0405
MA0160.10.142
MA0162.10.78
MA0163.16.54629e-8
MA0164.10.563
MA0258.10.029
MA0259.10.703



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: CNhs13533

Novel motifP-value
10.102
100.0273
1000.855
1010.906
1020.972
1030.243
1040.531
1050.125
1065.53974e-4
1070.212
1080.624
1090.382
110.193
1100.197
1110.167
1120.456
1130.474
1140.0383
1150.163
1160.998
1170.0892
1180.259
1190.197
120.272
1200.768
1210.655
1220.671
1230.812
1240.762
1250.296
1260.272
1270.521
1280.0651
1290.415
130.11
1300.439
1310.988
1320.0738
1330.722
1340.593
1350.837
1360.844
1370.0225
1380.435
1390.162
140.52
1400.442
1410.271
1420.158
1430.0321
1440.475
1450.357
1460.839
1470.761
1480.00883
1490.859
150.193
1500.304
1510.674
1520.448
1530.708
1540.747
1550.824
1560.746
1570.647
1580.0502
1590.118
160.374
1600.47
1610.403
1620.222
1630.103
1640.16
1650.174
1660.938
1670.309
1680.07
1690.0348
170.27
180.102
190.608
20.446
200.211
210.788
220.356
230.0332
240.325
250.442
260.0966
270.566
280.336
290.288
30.152
300.457
310.752
320.376
330.236
340.692
350.0989
360.0825
370.0662
380.389
390.845
40.927
400.259
410.0202
420.299
430.0206
440.522
450.673
460.214
470.585
480.557
490.162
50.331
500.922
510.554
520.345
530.621
540.501
550.604
560.727
570.864
580.147
590.214
60.793
600.0452
610.688
620.0877
630.612
640.577
650.224
660.414
670.423
680.5
690.212
70.234
700.0568
710.0296
720.179
730.269
740.0508
750.207
760.166
770.629
780.12
790.689
80.455
800.152
810.278
820.267
830.0191
840.0784
850.0505
860.0471
870.426
880.733
890.233
90.329
900.0907
910.376
920.299
930.581
940.114
950.538
960.377
970.507
980.171
990.0508



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: CNhs13533


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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