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FF:11873-125C1: 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, 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 numberD4-4
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-Peripheral0.139
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-0.119
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.329
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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-Whole0.244
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: CNhs13484

Jaspar motifP-value
MA0002.21.13982e-6
MA0003.10.297
MA0004.10.382
MA0006.10.799
MA0007.10.804
MA0009.10.254
MA0014.10.955
MA0017.10.0104
MA0018.20.439
MA0019.10.638
MA0024.18.41664e-4
MA0025.10.0304
MA0027.10.784
MA0028.10.164
MA0029.10.425
MA0030.10.563
MA0031.10.957
MA0035.20.537
MA0038.10.0195
MA0039.20.693
MA0040.10.338
MA0041.10.561
MA0042.10.822
MA0043.10.0189
MA0046.10.147
MA0047.20.45
MA0048.10.844
MA0050.13.35974e-4
MA0051.10.138
MA0052.10.911
MA0055.10.297
MA0057.10.727
MA0058.10.162
MA0059.10.489
MA0060.11.05446e-11
MA0061.10.00221
MA0062.20.315
MA0065.20.0194
MA0066.10.0802
MA0067.17.81356e-4
MA0068.10.194
MA0069.10.722
MA0070.10.05
MA0071.10.202
MA0072.10.738
MA0073.10.3
MA0074.10.212
MA0076.10.156
MA0077.10.183
MA0078.10.548
MA0079.20.789
MA0080.21.21096e-16
MA0081.13.78659e-4
MA0083.10.723
MA0084.10.779
MA0087.10.928
MA0088.10.496
MA0090.10.12
MA0091.10.372
MA0092.10.224
MA0093.10.378
MA0099.23.01452e-33
MA0100.10.671
MA0101.10.0505
MA0102.25.46054e-5
MA0103.10.714
MA0104.20.951
MA0105.15.03304e-6
MA0106.10.735
MA0107.10.0193
MA0108.20.0018
MA0111.10.308
MA0112.25.43569e-5
MA0113.10.991
MA0114.10.18
MA0115.10.616
MA0116.12.34896e-4
MA0117.10.319
MA0119.10.422
MA0122.10.629
MA0124.10.359
MA0125.10.392
MA0131.10.371
MA0135.10.292
MA0136.19.20282e-16
MA0137.20.772
MA0138.20.77
MA0139.10.78
MA0140.10.497
MA0141.10.0644
MA0142.10.57
MA0143.10.49
MA0144.10.238
MA0145.10.164
MA0146.10.0568
MA0147.10.984
MA0148.10.978
MA0149.10.196
MA0150.17.75027e-13
MA0152.10.279
MA0153.10.00583
MA0154.10.00205
MA0155.10.737
MA0156.11.77919e-8
MA0157.10.548
MA0159.10.0113
MA0160.10.0237
MA0162.10.966
MA0163.13.97054e-6
MA0164.10.747
MA0258.10.00248
MA0259.10.466



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: CNhs13484

Novel motifP-value
10.123
100.0241
1000.604
1010.611
1020.338
1030.244
1040.727
1050.335
1066.73142e-4
1070.14
1080.999
1090.22
110.2
1100.295
1110.0536
1120.192
1130.604
1140.0161
1150.236
1160.792
1170.0659
1180.189
1190.191
120.378
1200.921
1210.519
1220.51
1230.0585
1240.816
1250.83
1260.253
1270.252
1280.0206
1290.412
130.271
1300.133
1310.376
1320.0748
1330.94
1340.56
1350.219
1360.819
1370.00391
1380.174
1390.037
140.387
1400.119
1410.441
1420.964
1430.027
1440.834
1450.545
1460.62
1470.26
1480.0155
1490.598
150.157
1500.51
1510.281
1520.0821
1530.363
1540.383
1550.27
1560.88
1570.48
1580.0815
1590.739
160.326
1600.473
1610.596
1620.364
1630.605
1640.175
1650.141
1660.504
1670.308
1680.466
1690.00913
170.16
180.173
190.257
20.823
200.447
210.208
220.155
230.0568
240.243
250.334
260.045
270.618
280.416
290.386
30.0713
300.701
310.674
320.831
330.625
340.309
350.201
360.256
370.0675
380.299
390.728
40.723
400.306
410.0134
420.37
430.0509
440.694
450.61
460.124
470.584
480.484
490.116
50.207
500.976
510.317
520.259
530.244
540.274
550.202
560.631
570.769
580.0781
590.0892
60.587
600.0385
610.423
620.0268
630.465
640.421
650.199
660.345
670.426
680.773
690.638
70.252
700.0162
710.0355
720.246
730.0894
740.0425
750.0802
760.285
770.371
780.0865
790.0912
80.361
800.237
810.399
820.0839
830.145
840.663
850.00833
860.0356
870.365
880.409
890.31
90.332
900.0722
910.349
920.144
930.143
940.033
950.405
960.543
970.999
980.142
990.159



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: CNhs13484


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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