The Antisense Transcriptomes Of Cells


Ontology type: sgo:Patent     


Patent Info

DATE

2010-06-10T00:00

AUTHORS

VOGELSTEIN, BERT , KINZLER, KENNETH W. , HE, YIPING , VELCULESCU, VICTOR , PAPADOPOULOS, NICKOLAS

ABSTRACT

Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the Plus- or Minus-strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was non-random across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation. More... »

Related SciGraph Publications

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/2620", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "name": "VOGELSTEIN, BERT", 
        "type": "Person"
      }, 
      {
        "name": "KINZLER, KENNETH W.", 
        "type": "Person"
      }, 
      {
        "name": "HE, YIPING", 
        "type": "Person"
      }, 
      {
        "name": "VELCULESCU, VICTOR", 
        "type": "Person"
      }, 
      {
        "name": "PAPADOPOULOS, NICKOLAS", 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1152/physiolgenomics.00127.2006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002502551"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1537-2995.2007.01198.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018012159"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1163853", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023538121"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1163853", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023538121"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gki901", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024763851"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1223", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048586936", 
          "https://doi.org/10.1038/nmeth.1223"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2010-06-10T00:00", 
    "description": "

Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the Plus- or Minus-strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was non-random across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation.

", "id": "sg:patent.WO-2010065576-A2", "keywords": [ "Transcriptome", "transcription", "mammalian cell", "genome-wide level", "individual", "strand", "chromosome", "distinction", "transcript", "antisense transcript", "technique", "DNA strand", "origin", "RNA transcript", "expressed gene", "global level", "human cell type", "found evidence", "human gene", "distribution", "non-random", "genome", "cell type", "pervasive feature", "human cell", "fundamental component", "gene regulation" ], "name": "THE ANTISENSE TRANSCRIPTOMES OF CELLS", "recipient": [ { "id": "https://www.grid.ac/institutes/grid.21107.35", "type": "Organization" } ], "sameAs": [ "https://app.dimensions.ai/details/patent/WO-2010065576-A2" ], "sdDataset": "patents", "sdDatePublished": "2019-04-18T10:05", "sdLicense": "https://scigraph.springernature.com/explorer/license/", "sdPublisher": { "name": "Springer Nature - SN SciGraph project", "type": "Organization" }, "sdSource": "s3://com-uberresearch-data-patents-target-20190320-rc/data/sn-export/402f166718b70575fb5d4ffe01f064d1/0000100128-0000352499/json_export_00071.jsonl", "type": "Patent" } ]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/patent.WO-2010065576-A2'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/patent.WO-2010065576-A2'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/patent.WO-2010065576-A2'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/patent.WO-2010065576-A2'


 

This table displays all metadata directly associated to this object as RDF triples.

81 TRIPLES      15 PREDICATES      46 URIs      35 LITERALS      2 BLANK NODES

Subject Predicate Object
1 sg:patent.WO-2010065576-A2 schema:about anzsrc-for:2620
2 schema:author N29241163b07242f3b865a3ec7b7391ff
3 schema:citation sg:pub.10.1038/nmeth.1223
4 https://doi.org/10.1093/nar/gki901
5 https://doi.org/10.1111/j.1537-2995.2007.01198.x
6 https://doi.org/10.1126/science.1163853
7 https://doi.org/10.1152/physiolgenomics.00127.2006
8 schema:datePublished 2010-06-10T00:00
9 schema:description <p>Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the Plus- or Minus-strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was non-random across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation.</p>
10 schema:keywords DNA strand
11 RNA transcript
12 Transcriptome
13 antisense transcript
14 cell type
15 chromosome
16 distinction
17 distribution
18 expressed gene
19 found evidence
20 fundamental component
21 gene regulation
22 genome
23 genome-wide level
24 global level
25 human cell
26 human cell type
27 human gene
28 individual
29 mammalian cell
30 non-random
31 origin
32 pervasive feature
33 strand
34 technique
35 transcript
36 transcription
37 schema:name THE ANTISENSE TRANSCRIPTOMES OF CELLS
38 schema:recipient https://www.grid.ac/institutes/grid.21107.35
39 schema:sameAs https://app.dimensions.ai/details/patent/WO-2010065576-A2
40 schema:sdDatePublished 2019-04-18T10:05
41 schema:sdLicense https://scigraph.springernature.com/explorer/license/
42 schema:sdPublisher N09f3f12804a543ce86a9dc59be133a97
43 sgo:license sg:explorer/license/
44 sgo:sdDataset patents
45 rdf:type sgo:Patent
46 N0108c3be41694a8cb6d99ea4ec14b2c1 schema:name KINZLER, KENNETH W.
47 rdf:type schema:Person
48 N09f3f12804a543ce86a9dc59be133a97 schema:name Springer Nature - SN SciGraph project
49 rdf:type schema:Organization
50 N257b6c4c186a4b0c87ea0c9ed5697402 schema:name VOGELSTEIN, BERT
51 rdf:type schema:Person
52 N29241163b07242f3b865a3ec7b7391ff rdf:first N257b6c4c186a4b0c87ea0c9ed5697402
53 rdf:rest N4eee24b933194faa9831ccd1512c23fe
54 N35d344cba20147b68dcdbbe19d49c64c schema:name HE, YIPING
55 rdf:type schema:Person
56 N3cc185e664c84142a7060048d7eab90a rdf:first N559d114dd9ab471f9d605aae60aaabd9
57 rdf:rest Nbf3fefc42f0f46ff9cc402c5acc2d1ab
58 N4eee24b933194faa9831ccd1512c23fe rdf:first N0108c3be41694a8cb6d99ea4ec14b2c1
59 rdf:rest N6f622181df374f11a42ae7d01afe6f0b
60 N559d114dd9ab471f9d605aae60aaabd9 schema:name VELCULESCU, VICTOR
61 rdf:type schema:Person
62 N6f622181df374f11a42ae7d01afe6f0b rdf:first N35d344cba20147b68dcdbbe19d49c64c
63 rdf:rest N3cc185e664c84142a7060048d7eab90a
64 Nb992f8850ff043c8ad8a55236cbd9d92 schema:name PAPADOPOULOS, NICKOLAS
65 rdf:type schema:Person
66 Nbf3fefc42f0f46ff9cc402c5acc2d1ab rdf:first Nb992f8850ff043c8ad8a55236cbd9d92
67 rdf:rest rdf:nil
68 anzsrc-for:2620 schema:inDefinedTermSet anzsrc-for:
69 rdf:type schema:DefinedTerm
70 sg:pub.10.1038/nmeth.1223 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048586936
71 https://doi.org/10.1038/nmeth.1223
72 rdf:type schema:CreativeWork
73 https://doi.org/10.1093/nar/gki901 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024763851
74 rdf:type schema:CreativeWork
75 https://doi.org/10.1111/j.1537-2995.2007.01198.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1018012159
76 rdf:type schema:CreativeWork
77 https://doi.org/10.1126/science.1163853 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023538121
78 rdf:type schema:CreativeWork
79 https://doi.org/10.1152/physiolgenomics.00127.2006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002502551
80 rdf:type schema:CreativeWork
81 https://www.grid.ac/institutes/grid.21107.35 schema:Organization
 




Preview window. Press ESC to close (or click here)


...