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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-89 Sentence denotes U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line.
T2 90-216 Sentence denotes U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades.
T3 217-483 Sentence denotes In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30x genomic sequence coverage using a novel 50-base mate paired strategy with a 1.4kb mean insert library.
T4 484-600 Sentence denotes A total of 1,014,984,286 mate-end and 120,691,623 single-end two-base encoded reads were generated from five slides.
T5 601-754 Sentence denotes All data were aligned using a custom designed tool called BFAST, allowing optimal color space read alignment and accurate identification of DNA variants.
T6 755-1008 Sentence denotes The aligned sequence reads and mate-pair information identified 35 interchromosomal translocation events, 1,315 structural variations (>100 bp), 191,743 small (<21 bp) insertions and deletions (indels), and 2,384,470 single nucleotide variations (SNVs).
T7 1009-1180 Sentence denotes Among these observations, the known homozygous mutation in PTEN was robustly identified, and genes involved in cell adhesion were overrepresented in the mutated gene list.
T8 1181-1319 Sentence denotes Data were compared to 219,187 heterozygous single nucleotide polymorphisms assayed by Illumina 1M Duo genotyping array to assess accuracy:
T9 1320-1435 Sentence denotes 93.83% of all SNPs were reliably detected at filtering thresholds that yield greater than 99.99% sequence accuracy.
T10 1436-1572 Sentence denotes Protein coding sequences were disrupted predominantly in this cancer cell line due to small indels, large deletions, and translocations.
T11 1573-1779 Sentence denotes In total, 512 genes were homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions, and 35 by interchromosomal translocations to reveal a highly mutated cell line genome.
T12 1780-1884 Sentence denotes Of the small homozygously mutated variants, 8 SNVs and 99 indels were novel events not present in dbSNP.
T13 1885-2002 Sentence denotes These data demonstrate that routine generation of broad cancer genome sequence is possible outside of genome centers.
T14 2003-2124 Sentence denotes The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 66-71 OrganismTaxon denotes human NCBItxid:9606
T2 429-433 OrganismTaxon denotes mate NCBItxid:185542
T3 509-513 OrganismTaxon denotes mate NCBItxid:185542
T4 786-790 OrganismTaxon denotes mate NCBItxid:185542

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
7071 0-5 CellLine denotes U87MG NCBITaxon:9606
7072 66-71 OrganismTaxon denotes human NCBITaxon:9606
7073 72-78 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
7074 90-95 CellLine denotes U87MG NCBITaxon:9606
7075 118-133 DiseaseOrPhenotypicFeature denotes grade IV glioma MESH:D005909
7076 320-326 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
7077 1068-1072 GeneOrGeneProduct denotes PTEN NCBIGene:5728
7078 1498-1504 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
7079 1941-1947 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
7080 2028-2033 CellLine denotes U87MG NCBITaxon:9606

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 72-78 DiseaseOrPhenotypicFeature denotes cancer 0004992
T2 127-133 DiseaseOrPhenotypicFeature denotes glioma 0021042
T3 320-326 DiseaseOrPhenotypicFeature denotes cancer 0004992
T4 1498-1504 DiseaseOrPhenotypicFeature denotes cancer 0004992
T5 1941-1947 DiseaseOrPhenotypicFeature denotes cancer 0004992

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 79-83 GeneOrGeneProduct denotes cell
T2 84-88 GeneOrGeneProduct denotes line
T3 134-138 GeneOrGeneProduct denotes cell
T4 139-143 GeneOrGeneProduct denotes line
T5 208-215 GeneOrGeneProduct denotes decades
T6 277-281 GeneOrGeneProduct denotes cell
T7 282-286 GeneOrGeneProduct denotes line
T8 294-299 GeneOrGeneProduct denotes serve
T9 314-319 GeneOrGeneProduct denotes broad
T10 415-420 GeneOrGeneProduct denotes novel
T11 424-428 GeneOrGeneProduct denotes base
T12 429-433 GeneOrGeneProduct denotes mate
T13 434-440 GeneOrGeneProduct denotes paired
T14 486-491 GeneOrGeneProduct denotes total
T15 509-513 GeneOrGeneProduct denotes mate
T16 514-517 GeneOrGeneProduct denotes end
T17 541-544 GeneOrGeneProduct denotes end
T18 549-553 GeneOrGeneProduct denotes base
T19 601-604 GeneOrGeneProduct denotes All
T20 652-658 GeneOrGeneProduct denotes called
T21 786-790 GeneOrGeneProduct denotes mate
T22 791-795 GeneOrGeneProduct denotes pair
T23 839-852 GeneOrGeneProduct denotes translocation
T24 908-913 GeneOrGeneProduct denotes small
T25 1056-1064 GeneOrGeneProduct denotes mutation
T26 1068-1072 GeneOrGeneProduct denotes PTEN
T27 1120-1124 GeneOrGeneProduct denotes cell
T28 1125-1133 GeneOrGeneProduct denotes adhesion
T29 1162-1169 GeneOrGeneProduct denotes mutated
T30 1175-1179 GeneOrGeneProduct denotes list
T31 1330-1333 GeneOrGeneProduct denotes all
T32 1391-1396 GeneOrGeneProduct denotes yield
T33 1436-1443 GeneOrGeneProduct denotes Protein
T34 1466-1475 GeneOrGeneProduct denotes disrupted
T35 1505-1509 GeneOrGeneProduct denotes cell
T36 1510-1514 GeneOrGeneProduct denotes line
T37 1522-1527 GeneOrGeneProduct denotes small
T38 1536-1541 GeneOrGeneProduct denotes large
T39 1557-1571 GeneOrGeneProduct denotes translocations
T40 1576-1581 GeneOrGeneProduct denotes total
T41 1611-1618 GeneOrGeneProduct denotes mutated
T42 1650-1655 GeneOrGeneProduct denotes small
T43 1671-1676 GeneOrGeneProduct denotes large
T44 1720-1734 GeneOrGeneProduct denotes translocations
T45 1747-1753 GeneOrGeneProduct denotes highly
T46 1754-1761 GeneOrGeneProduct denotes mutated
T47 1762-1766 GeneOrGeneProduct denotes cell
T48 1767-1771 GeneOrGeneProduct denotes line
T49 1787-1792 GeneOrGeneProduct denotes small
T50 1806-1813 GeneOrGeneProduct denotes mutated
T51 1850-1855 GeneOrGeneProduct denotes novel
T52 1935-1940 GeneOrGeneProduct denotes broad
T53 1976-1983 GeneOrGeneProduct denotes outside
T54 2065-2078 GeneOrGeneProduct denotes of mutational
T55 2106-2110 GeneOrGeneProduct denotes cell
T56 2111-2115 GeneOrGeneProduct denotes line

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 79-83 GeneOrGeneProduct denotes cell
T2 134-138 GeneOrGeneProduct denotes cell
T3 277-281 GeneOrGeneProduct denotes cell
T4 314-319 GeneOrGeneProduct denotes broad
T5 415-420 GeneOrGeneProduct denotes novel
T6 429-433 GeneOrGeneProduct denotes mate
T7 434-440 GeneOrGeneProduct denotes paired
T8 509-513 GeneOrGeneProduct denotes mate
T9 786-790 GeneOrGeneProduct denotes mate
T10 839-852 GeneOrGeneProduct denotes translocation
T11 908-913 GeneOrGeneProduct denotes small
T12 1068-1072 GeneOrGeneProduct denotes PTEN
T13 1120-1124 GeneOrGeneProduct denotes cell
T14 1125-1133 GeneOrGeneProduct denotes adhesion
T15 1436-1443 GeneOrGeneProduct denotes Protein
T16 1466-1475 GeneOrGeneProduct denotes disrupted
T17 1505-1509 GeneOrGeneProduct denotes cell
T18 1522-1527 GeneOrGeneProduct denotes small
T19 1536-1541 GeneOrGeneProduct denotes large
T20 1557-1571 GeneOrGeneProduct denotes translocations
T21 1650-1655 GeneOrGeneProduct denotes small
T22 1671-1676 GeneOrGeneProduct denotes large
T23 1720-1734 GeneOrGeneProduct denotes translocations
T24 1762-1766 GeneOrGeneProduct denotes cell
T25 1787-1792 GeneOrGeneProduct denotes small
T26 1850-1855 GeneOrGeneProduct denotes novel
T27 1935-1940 GeneOrGeneProduct denotes broad
T28 2106-2110 GeneOrGeneProduct denotes cell

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 41-65 DiseaseOrPhenotypicFeature denotes cytogenetically aberrant D002869
T2 72-78 DiseaseOrPhenotypicFeature denotes cancer D009369
T3 127-133 DiseaseOrPhenotypicFeature denotes glioma D005910
T4 320-326 DiseaseOrPhenotypicFeature denotes cancer D009369
T5 1498-1504 DiseaseOrPhenotypicFeature denotes cancer D009369
T6 1941-1947 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 1068-1072 GeneOrGeneProduct denotes PTEN
T2 1436-1450 GeneOrGeneProduct denotes Protein coding

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 127-133 DiseaseOrPhenotypicFeature denotes glioma 0100342|0021042
T3 695-699 DiseaseOrPhenotypicFeature denotes read 0002169

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 72-78 DiseaseOrPhenotypicFeature denotes cancer D009369
T2 127-133 DiseaseOrPhenotypicFeature denotes glioma D005910
T3 320-326 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 1498-1504 DiseaseOrPhenotypicFeature denotes cancer D009369
T5 1941-1947 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin_CellLine

Id Subject Object Predicate Lexical cue cellosaurus_accession_id
T1 0-5 CellLine denotes U87MG CVCL_0022|CVCL_GP63
T3 90-95 CellLine denotes U87MG CVCL_0022|CVCL_GP63
T5 2028-2033 CellLine denotes U87MG CVCL_0022|CVCL_GP63

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 72-78 DiseaseOrPhenotypicFeature denotes cancer D009369
T2 127-133 DiseaseOrPhenotypicFeature denotes glioma D005910
T3 320-326 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 1498-1504 DiseaseOrPhenotypicFeature denotes cancer D009369
T5 1941-1947 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 66-71 OrganismTaxon denotes human
T2 429-433 OrganismTaxon denotes mate
T3 509-513 OrganismTaxon denotes mate
T4 786-790 OrganismTaxon denotes mate

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label cellosaurus_accession_id
T5 2028-2033 CellLine denotes U87MG CVCL_GP63|CVCL_0022
T3 90-95 CellLine denotes U87MG CVCL_GP63|CVCL_0022
T1 0-5 CellLine denotes U87MG CVCL_GP63|CVCL_0022
T2 1436-1450 GeneOrGeneProduct denotes Protein coding
T59820 1068-1072 GeneOrGeneProduct denotes PTEN
T37866 1941-1947 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 1498-1504 DiseaseOrPhenotypicFeature denotes cancer D009369
T49139 320-326 DiseaseOrPhenotypicFeature denotes cancer D009369
T75302 127-133 DiseaseOrPhenotypicFeature denotes glioma D005910
T16638 72-78 DiseaseOrPhenotypicFeature denotes cancer D009369
T2749 786-790 OrganismTaxon denotes mate
T96170 509-513 OrganismTaxon denotes mate
T14170 429-433 OrganismTaxon denotes mate
T96974 66-71 OrganismTaxon denotes human

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 127-133 HP_0009733 denotes glioma
T2 320-326 HP_0002664 denotes cancer
T3 1498-1504 HP_0002664 denotes cancer
T4 1941-1947 HP_0002664 denotes cancer

Allie

Id Subject Object Predicate Lexical cue
SS1_20126413_5_0 972-1000 expanded denotes single nucleotide variations
SS2_20126413_5_0 1002-1006 abbr denotes SNVs
AE1_20126413_5_0 SS1_20126413_5_0 SS2_20126413_5_0 abbreviatedTo single nucleotide variations,SNVs