TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites Article Swipe
Tsu-Pei Chiu
,
Beibei Xin
,
Nicholas Markarian
,
Yingfei Wang
,
Remo Rohs
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkz970
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkz970
TFBSshape (https://tfbsshape.usc.edu) is a motif database for analyzing structural profiles of transcription factor binding sites (TFBSs). The main rationale for this database is to be able to derive mechanistic insights in protein–DNA readout modes from sequencing data without available structures. We extended the quantity and dimensionality of TFBSshape, from mostly in vitro to in vivo binding and from unmethylated to methylated DNA. This new release of TFBSshape improves its functionality and launches a responsive and user-friendly web interface for easy access to the data. The current expansion includes new entries from the most recent collections of transcription factors (TFs) from the JASPAR and UniPROBE databases, methylated TFBSs derived from in vitro high-throughput EpiSELEX-seq binding assays and in vivo methylated TFBSs from the MeDReaders database. TFBSshape content has increased to 2428 structural profiles for 1900 TFs from 39 different species. The structural profiles for each TFBS entry now include 13 shape features and minor groove electrostatic potential for standard DNA and four shape features for methylated DNA. We improved the flexibility and accuracy for the shape-based alignment of TFBSs and designed new tools to compare methylated and unmethylated structural profiles of TFs and methods to derive DNA shape-preserving nucleotide mutations in TFBSs.
Related Topics
Concepts
DNA binding site
Biology
Database
Binding site
DNA
Transcription factor
Computational biology
Genetics
Promoter
Gene
Computer science
Gene expression
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkz970
- https://academic.oup.com/nar/article-pdf/48/D1/D246/31697977/gkz970.pdf
- OA Status
- gold
- Cited By
- 41
- References
- 60
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2982572594
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W2982572594Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nar/gkz970Digital Object Identifier
- Title
-
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sitesWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2019Year of publication
- Publication date
-
2019-10-11Full publication date if available
- Authors
-
Tsu-Pei Chiu, Beibei Xin, Nicholas Markarian, Yingfei Wang, Remo RohsList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gkz970Publisher landing page
- PDF URL
-
https://academic.oup.com/nar/article-pdf/48/D1/D246/31697977/gkz970.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/nar/article-pdf/48/D1/D246/31697977/gkz970.pdfDirect OA link when available
- Concepts
-
DNA binding site, Biology, Database, Binding site, DNA, Transcription factor, Computational biology, Genetics, Promoter, Gene, Computer science, Gene expressionTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
41Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 5, 2024: 8, 2023: 3, 2022: 5, 2021: 9Per-year citation counts (last 5 years)
- References (count)
-
60Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W2982572594 |
|---|---|
| doi | https://doi.org/10.1093/nar/gkz970 |
| ids.doi | https://doi.org/10.1093/nar/gkz970 |
| ids.mag | 2982572594 |
| ids.pmid | https://pubmed.ncbi.nlm.nih.gov/31665425 |
| ids.openalex | https://openalex.org/W2982572594 |
| fwci | 2.6793262 |
| mesh[0].qualifier_ui | |
| mesh[0].descriptor_ui | D001665 |
| mesh[0].is_major_topic | False |
| mesh[0].qualifier_name | |
| mesh[0].descriptor_name | Binding Sites |
| mesh[1].qualifier_ui | Q000737 |
| mesh[1].descriptor_ui | D004247 |
| mesh[1].is_major_topic | False |
| mesh[1].qualifier_name | chemistry |
| mesh[1].descriptor_name | DNA |
| mesh[2].qualifier_ui | Q000378 |
| mesh[2].descriptor_ui | D004247 |
| mesh[2].is_major_topic | False |
| mesh[2].qualifier_name | metabolism |
| mesh[2].descriptor_name | DNA |
| mesh[3].qualifier_ui | |
| mesh[3].descriptor_ui | D019175 |
| mesh[3].is_major_topic | False |
| mesh[3].qualifier_name | |
| mesh[3].descriptor_name | DNA Methylation |
| mesh[4].qualifier_ui | |
| mesh[4].descriptor_ui | D030541 |
| mesh[4].is_major_topic | True |
| mesh[4].qualifier_name | |
| mesh[4].descriptor_name | Databases, Genetic |
| mesh[5].qualifier_ui | |
| mesh[5].descriptor_ui | D009154 |
| mesh[5].is_major_topic | False |
| mesh[5].qualifier_name | |
| mesh[5].descriptor_name | Mutation |
| mesh[6].qualifier_ui | |
| mesh[6].descriptor_ui | D059372 |
| mesh[6].is_major_topic | False |
| mesh[6].qualifier_name | |
| mesh[6].descriptor_name | Nucleotide Motifs |
| mesh[7].qualifier_ui | |
| mesh[7].descriptor_ui | D011485 |
| mesh[7].is_major_topic | False |
| mesh[7].qualifier_name | |
| mesh[7].descriptor_name | Protein Binding |
| mesh[8].qualifier_ui | |
| mesh[8].descriptor_ui | D017422 |
| mesh[8].is_major_topic | False |
| mesh[8].qualifier_name | |
| mesh[8].descriptor_name | Sequence Analysis, DNA |
| mesh[9].qualifier_ui | Q000378 |
| mesh[9].descriptor_ui | D014157 |
| mesh[9].is_major_topic | False |
| mesh[9].qualifier_name | metabolism |
| mesh[9].descriptor_name | Transcription Factors |
| mesh[10].qualifier_ui | |
| mesh[10].descriptor_ui | D001665 |
| mesh[10].is_major_topic | False |
| mesh[10].qualifier_name | |
| mesh[10].descriptor_name | Binding Sites |
| mesh[11].qualifier_ui | Q000737 |
| mesh[11].descriptor_ui | D004247 |
| mesh[11].is_major_topic | False |
| mesh[11].qualifier_name | chemistry |
| mesh[11].descriptor_name | DNA |
| mesh[12].qualifier_ui | Q000378 |
| mesh[12].descriptor_ui | D004247 |
| mesh[12].is_major_topic | False |
| mesh[12].qualifier_name | metabolism |
| mesh[12].descriptor_name | DNA |
| mesh[13].qualifier_ui | |
| mesh[13].descriptor_ui | D019175 |
| mesh[13].is_major_topic | False |
| mesh[13].qualifier_name | |
| mesh[13].descriptor_name | DNA Methylation |
| mesh[14].qualifier_ui | |
| mesh[14].descriptor_ui | D030541 |
| mesh[14].is_major_topic | True |
| mesh[14].qualifier_name | |
| mesh[14].descriptor_name | Databases, Genetic |
| mesh[15].qualifier_ui | |
| mesh[15].descriptor_ui | D009154 |
| mesh[15].is_major_topic | False |
| mesh[15].qualifier_name | |
| mesh[15].descriptor_name | Mutation |
| mesh[16].qualifier_ui | |
| mesh[16].descriptor_ui | D059372 |
| mesh[16].is_major_topic | False |
| mesh[16].qualifier_name | |
| mesh[16].descriptor_name | Nucleotide Motifs |
| mesh[17].qualifier_ui | |
| mesh[17].descriptor_ui | D011485 |
| mesh[17].is_major_topic | False |
| mesh[17].qualifier_name | |
| mesh[17].descriptor_name | Protein Binding |
| mesh[18].qualifier_ui | |
| mesh[18].descriptor_ui | D017422 |
| mesh[18].is_major_topic | False |
| mesh[18].qualifier_name | |
| mesh[18].descriptor_name | Sequence Analysis, DNA |
| mesh[19].qualifier_ui | Q000378 |
| mesh[19].descriptor_ui | D014157 |
| mesh[19].is_major_topic | False |
| mesh[19].qualifier_name | metabolism |
| mesh[19].descriptor_name | Transcription Factors |
| type | article |
| title | TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites |
| awards[0].id | https://openalex.org/G1325023930 |
| awards[0].funder_id | https://openalex.org/F4320332161 |
| awards[0].display_name | |
| awards[0].funder_award_id | R01GM106056 |
| awards[0].funder_display_name | National Institutes of Health |
| awards[1].id | https://openalex.org/G1053525483 |
| awards[1].funder_id | https://openalex.org/F4320332161 |
| awards[1].display_name | |
| awards[1].funder_award_id | R35GM130376 |
| awards[1].funder_display_name | National Institutes of Health |
| awards[2].id | https://openalex.org/G3118094023 |
| awards[2].funder_id | https://openalex.org/F4320332161 |
| awards[2].display_name | |
| awards[2].funder_award_id | R01HG003008 |
| awards[2].funder_display_name | National Institutes of Health |
| awards[3].id | https://openalex.org/G7238104403 |
| awards[3].funder_id | https://openalex.org/F4320307846 |
| awards[3].display_name | Quantitative dissection of molecular determinants of enhancer function |
| awards[3].funder_award_id | RGP0021/2018 |
| awards[3].funder_display_name | Human Frontier Science Program |
| biblio.issue | D1 |
| biblio.volume | 48 |
| biblio.last_page | D255 |
| biblio.first_page | D246 |
| topics[0].id | https://openalex.org/T10222 |
| topics[0].field.id | https://openalex.org/fields/13 |
| topics[0].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[0].score | 1.0 |
| topics[0].domain.id | https://openalex.org/domains/1 |
| topics[0].domain.display_name | Life Sciences |
| topics[0].subfield.id | https://openalex.org/subfields/1312 |
| topics[0].subfield.display_name | Molecular Biology |
| topics[0].display_name | Genomics and Chromatin Dynamics |
| topics[1].id | https://openalex.org/T10521 |
| topics[1].field.id | https://openalex.org/fields/13 |
| topics[1].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[1].score | 0.9988999962806702 |
| topics[1].domain.id | https://openalex.org/domains/1 |
| topics[1].domain.display_name | Life Sciences |
| topics[1].subfield.id | https://openalex.org/subfields/1312 |
| topics[1].subfield.display_name | Molecular Biology |
| topics[1].display_name | RNA and protein synthesis mechanisms |
| topics[2].id | https://openalex.org/T10269 |
| topics[2].field.id | https://openalex.org/fields/13 |
| topics[2].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[2].score | 0.9980000257492065 |
| topics[2].domain.id | https://openalex.org/domains/1 |
| topics[2].domain.display_name | Life Sciences |
| topics[2].subfield.id | https://openalex.org/subfields/1312 |
| topics[2].subfield.display_name | Molecular Biology |
| topics[2].display_name | Epigenetics and DNA Methylation |
| funders[0].id | https://openalex.org/F4320307846 |
| funders[0].ror | https://ror.org/02ebx7v45 |
| funders[0].display_name | Human Frontier Science Program |
| funders[1].id | https://openalex.org/F4320315928 |
| funders[1].ror | |
| funders[1].display_name | Rose Hills Foundation |
| funders[2].id | https://openalex.org/F4320332161 |
| funders[2].ror | https://ror.org/01cwqze88 |
| funders[2].display_name | National Institutes of Health |
| is_xpac | False |
| apc_list.value | 3630 |
| apc_list.currency | USD |
| apc_list.value_usd | 3630 |
| apc_paid.value | 3630 |
| apc_paid.currency | USD |
| apc_paid.value_usd | 3630 |
| concepts[0].id | https://openalex.org/C3662595 |
| concepts[0].level | 5 |
| concepts[0].score | 0.7463475465774536 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q5205743 |
| concepts[0].display_name | DNA binding site |
| concepts[1].id | https://openalex.org/C86803240 |
| concepts[1].level | 0 |
| concepts[1].score | 0.7143653631210327 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[1].display_name | Biology |
| concepts[2].id | https://openalex.org/C77088390 |
| concepts[2].level | 1 |
| concepts[2].score | 0.6333905458450317 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q8513 |
| concepts[2].display_name | Database |
| concepts[3].id | https://openalex.org/C107824862 |
| concepts[3].level | 2 |
| concepts[3].score | 0.5511351823806763 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q616005 |
| concepts[3].display_name | Binding site |
| concepts[4].id | https://openalex.org/C552990157 |
| concepts[4].level | 2 |
| concepts[4].score | 0.5488043427467346 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q7430 |
| concepts[4].display_name | DNA |
| concepts[5].id | https://openalex.org/C86339819 |
| concepts[5].level | 3 |
| concepts[5].score | 0.49796199798583984 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q407384 |
| concepts[5].display_name | Transcription factor |
| concepts[6].id | https://openalex.org/C70721500 |
| concepts[6].level | 1 |
| concepts[6].score | 0.4858402907848358 |
| concepts[6].wikidata | https://www.wikidata.org/wiki/Q177005 |
| concepts[6].display_name | Computational biology |
| concepts[7].id | https://openalex.org/C54355233 |
| concepts[7].level | 1 |
| concepts[7].score | 0.3677695095539093 |
| concepts[7].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[7].display_name | Genetics |
| concepts[8].id | https://openalex.org/C101762097 |
| concepts[8].level | 4 |
| concepts[8].score | 0.31881582736968994 |
| concepts[8].wikidata | https://www.wikidata.org/wiki/Q224093 |
| concepts[8].display_name | Promoter |
| concepts[9].id | https://openalex.org/C104317684 |
| concepts[9].level | 2 |
| concepts[9].score | 0.2649136483669281 |
| concepts[9].wikidata | https://www.wikidata.org/wiki/Q7187 |
| concepts[9].display_name | Gene |
| concepts[10].id | https://openalex.org/C41008148 |
| concepts[10].level | 0 |
| concepts[10].score | 0.16521331667900085 |
| concepts[10].wikidata | https://www.wikidata.org/wiki/Q21198 |
| concepts[10].display_name | Computer science |
| concepts[11].id | https://openalex.org/C150194340 |
| concepts[11].level | 3 |
| concepts[11].score | 0.14219292998313904 |
| concepts[11].wikidata | https://www.wikidata.org/wiki/Q26972 |
| concepts[11].display_name | Gene expression |
| keywords[0].id | https://openalex.org/keywords/dna-binding-site |
| keywords[0].score | 0.7463475465774536 |
| keywords[0].display_name | DNA binding site |
| keywords[1].id | https://openalex.org/keywords/biology |
| keywords[1].score | 0.7143653631210327 |
| keywords[1].display_name | Biology |
| keywords[2].id | https://openalex.org/keywords/database |
| keywords[2].score | 0.6333905458450317 |
| keywords[2].display_name | Database |
| keywords[3].id | https://openalex.org/keywords/binding-site |
| keywords[3].score | 0.5511351823806763 |
| keywords[3].display_name | Binding site |
| keywords[4].id | https://openalex.org/keywords/dna |
| keywords[4].score | 0.5488043427467346 |
| keywords[4].display_name | DNA |
| keywords[5].id | https://openalex.org/keywords/transcription-factor |
| keywords[5].score | 0.49796199798583984 |
| keywords[5].display_name | Transcription factor |
| keywords[6].id | https://openalex.org/keywords/computational-biology |
| keywords[6].score | 0.4858402907848358 |
| keywords[6].display_name | Computational biology |
| keywords[7].id | https://openalex.org/keywords/genetics |
| keywords[7].score | 0.3677695095539093 |
| keywords[7].display_name | Genetics |
| keywords[8].id | https://openalex.org/keywords/promoter |
| keywords[8].score | 0.31881582736968994 |
| keywords[8].display_name | Promoter |
| keywords[9].id | https://openalex.org/keywords/gene |
| keywords[9].score | 0.2649136483669281 |
| keywords[9].display_name | Gene |
| keywords[10].id | https://openalex.org/keywords/computer-science |
| keywords[10].score | 0.16521331667900085 |
| keywords[10].display_name | Computer science |
| keywords[11].id | https://openalex.org/keywords/gene-expression |
| keywords[11].score | 0.14219292998313904 |
| keywords[11].display_name | Gene expression |
| language | en |
| locations[0].id | doi:10.1093/nar/gkz970 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S134668137 |
| locations[0].source.issn | 0305-1048, 1362-4954, 1362-4962 |
| locations[0].source.type | journal |
| locations[0].source.is_oa | True |
| locations[0].source.issn_l | 0305-1048 |
| locations[0].source.is_core | True |
| locations[0].source.is_in_doaj | True |
| locations[0].source.display_name | Nucleic Acids Research |
| locations[0].source.host_organization | https://openalex.org/P4310311648 |
| locations[0].source.host_organization_name | Oxford University Press |
| locations[0].source.host_organization_lineage | https://openalex.org/P4310311648, https://openalex.org/P4310311647 |
| locations[0].source.host_organization_lineage_names | Oxford University Press, University of Oxford |
| locations[0].license | |
| locations[0].pdf_url | https://academic.oup.com/nar/article-pdf/48/D1/D246/31697977/gkz970.pdf |
| locations[0].version | publishedVersion |
| locations[0].raw_type | journal-article |
| locations[0].license_id | |
| locations[0].is_accepted | True |
| locations[0].is_published | True |
| locations[0].raw_source_name | Nucleic Acids Research |
| locations[0].landing_page_url | https://doi.org/10.1093/nar/gkz970 |
| locations[1].id | pmid:31665425 |
| locations[1].is_oa | False |
| locations[1].source.id | https://openalex.org/S4306525036 |
| locations[1].source.issn | |
| locations[1].source.type | repository |
| locations[1].source.is_oa | False |
| locations[1].source.issn_l | |
| locations[1].source.is_core | False |
| locations[1].source.is_in_doaj | False |
| locations[1].source.display_name | PubMed |
| locations[1].source.host_organization | https://openalex.org/I1299303238 |
| locations[1].source.host_organization_name | National Institutes of Health |
| locations[1].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[1].license | |
| locations[1].pdf_url | |
| locations[1].version | publishedVersion |
| locations[1].raw_type | |
| locations[1].license_id | |
| locations[1].is_accepted | True |
| locations[1].is_published | True |
| locations[1].raw_source_name | Nucleic acids research |
| locations[1].landing_page_url | https://pubmed.ncbi.nlm.nih.gov/31665425 |
| locations[2].id | pmh:oai:pubmedcentral.nih.gov:7145579 |
| locations[2].is_oa | True |
| locations[2].source.id | https://openalex.org/S2764455111 |
| locations[2].source.issn | |
| locations[2].source.type | repository |
| locations[2].source.is_oa | False |
| locations[2].source.issn_l | |
| locations[2].source.is_core | False |
| locations[2].source.is_in_doaj | False |
| locations[2].source.display_name | PubMed Central |
| locations[2].source.host_organization | https://openalex.org/I1299303238 |
| locations[2].source.host_organization_name | National Institutes of Health |
| locations[2].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[2].license | |
| locations[2].pdf_url | |
| locations[2].version | submittedVersion |
| locations[2].raw_type | Text |
| locations[2].license_id | |
| locations[2].is_accepted | False |
| locations[2].is_published | False |
| locations[2].raw_source_name | Nucleic Acids Res |
| locations[2].landing_page_url | https://www.ncbi.nlm.nih.gov/pmc/articles/7145579 |
| indexed_in | crossref, doaj, pubmed |
| authorships[0].author.id | https://openalex.org/A5047776299 |
| authorships[0].author.orcid | https://orcid.org/0000-0002-2472-6557 |
| authorships[0].author.display_name | Tsu-Pei Chiu |
| authorships[0].countries | US |
| authorships[0].affiliations[0].institution_ids | https://openalex.org/I1174212 |
| authorships[0].affiliations[0].raw_affiliation_string | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[0].institutions[0].id | https://openalex.org/I1174212 |
| authorships[0].institutions[0].ror | https://ror.org/03taz7m60 |
| authorships[0].institutions[0].type | education |
| authorships[0].institutions[0].lineage | https://openalex.org/I1174212 |
| authorships[0].institutions[0].country_code | US |
| authorships[0].institutions[0].display_name | University of Southern California |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Tsu-Pei Chiu |
| authorships[0].is_corresponding | False |
| authorships[0].raw_affiliation_strings | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[1].author.id | https://openalex.org/A5108840918 |
| authorships[1].author.orcid | |
| authorships[1].author.display_name | Beibei Xin |
| authorships[1].countries | US |
| authorships[1].affiliations[0].institution_ids | https://openalex.org/I1174212 |
| authorships[1].affiliations[0].raw_affiliation_string | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[1].institutions[0].id | https://openalex.org/I1174212 |
| authorships[1].institutions[0].ror | https://ror.org/03taz7m60 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I1174212 |
| authorships[1].institutions[0].country_code | US |
| authorships[1].institutions[0].display_name | University of Southern California |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Beibei Xin |
| authorships[1].is_corresponding | False |
| authorships[1].raw_affiliation_strings | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[2].author.id | https://openalex.org/A5087307742 |
| authorships[2].author.orcid | https://orcid.org/0000-0003-1347-2392 |
| authorships[2].author.display_name | Nicholas Markarian |
| authorships[2].countries | US |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I1174212 |
| authorships[2].affiliations[0].raw_affiliation_string | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[2].institutions[0].id | https://openalex.org/I1174212 |
| authorships[2].institutions[0].ror | https://ror.org/03taz7m60 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I1174212 |
| authorships[2].institutions[0].country_code | US |
| authorships[2].institutions[0].display_name | University of Southern California |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Nicholas Markarian |
| authorships[2].is_corresponding | False |
| authorships[2].raw_affiliation_strings | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[3].author.id | https://openalex.org/A5038576346 |
| authorships[3].author.orcid | https://orcid.org/0000-0002-8723-252X |
| authorships[3].author.display_name | Yingfei Wang |
| authorships[3].countries | US |
| authorships[3].affiliations[0].institution_ids | https://openalex.org/I1174212 |
| authorships[3].affiliations[0].raw_affiliation_string | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[3].institutions[0].id | https://openalex.org/I1174212 |
| authorships[3].institutions[0].ror | https://ror.org/03taz7m60 |
| authorships[3].institutions[0].type | education |
| authorships[3].institutions[0].lineage | https://openalex.org/I1174212 |
| authorships[3].institutions[0].country_code | US |
| authorships[3].institutions[0].display_name | University of Southern California |
| authorships[3].author_position | middle |
| authorships[3].raw_author_name | Yingfei Wang |
| authorships[3].is_corresponding | False |
| authorships[3].raw_affiliation_strings | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[4].author.id | https://openalex.org/A5019996279 |
| authorships[4].author.orcid | https://orcid.org/0000-0003-1752-1884 |
| authorships[4].author.display_name | Remo Rohs |
| authorships[4].countries | US |
| authorships[4].affiliations[0].institution_ids | https://openalex.org/I1174212 |
| authorships[4].affiliations[0].raw_affiliation_string | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| authorships[4].institutions[0].id | https://openalex.org/I1174212 |
| authorships[4].institutions[0].ror | https://ror.org/03taz7m60 |
| authorships[4].institutions[0].type | education |
| authorships[4].institutions[0].lineage | https://openalex.org/I1174212 |
| authorships[4].institutions[0].country_code | US |
| authorships[4].institutions[0].display_name | University of Southern California |
| authorships[4].author_position | last |
| authorships[4].raw_author_name | Remo Rohs |
| authorships[4].is_corresponding | True |
| authorships[4].raw_affiliation_strings | Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA |
| has_content.pdf | True |
| has_content.grobid_xml | True |
| is_paratext | False |
| open_access.is_oa | True |
| open_access.oa_url | https://academic.oup.com/nar/article-pdf/48/D1/D246/31697977/gkz970.pdf |
| open_access.oa_status | gold |
| open_access.any_repository_has_fulltext | False |
| created_date | 2025-10-10T00:00:00 |
| display_name | TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites |
| has_fulltext | False |
| is_retracted | False |
| updated_date | 2025-11-06T03:46:38.306776 |
| primary_topic.id | https://openalex.org/T10222 |
| primary_topic.field.id | https://openalex.org/fields/13 |
| primary_topic.field.display_name | Biochemistry, Genetics and Molecular Biology |
| primary_topic.score | 1.0 |
| primary_topic.domain.id | https://openalex.org/domains/1 |
| primary_topic.domain.display_name | Life Sciences |
| primary_topic.subfield.id | https://openalex.org/subfields/1312 |
| primary_topic.subfield.display_name | Molecular Biology |
| primary_topic.display_name | Genomics and Chromatin Dynamics |
| related_works | https://openalex.org/W2036927633, https://openalex.org/W2152664145, https://openalex.org/W2146517458, https://openalex.org/W2153561273, https://openalex.org/W2079197459, https://openalex.org/W2379997263, https://openalex.org/W2165899269, https://openalex.org/W2236968607, https://openalex.org/W2367493320, https://openalex.org/W2131580913 |
| cited_by_count | 41 |
| counts_by_year[0].year | 2025 |
| counts_by_year[0].cited_by_count | 5 |
| counts_by_year[1].year | 2024 |
| counts_by_year[1].cited_by_count | 8 |
| counts_by_year[2].year | 2023 |
| counts_by_year[2].cited_by_count | 3 |
| counts_by_year[3].year | 2022 |
| counts_by_year[3].cited_by_count | 5 |
| counts_by_year[4].year | 2021 |
| counts_by_year[4].cited_by_count | 9 |
| counts_by_year[5].year | 2020 |
| counts_by_year[5].cited_by_count | 8 |
| counts_by_year[6].year | 2019 |
| counts_by_year[6].cited_by_count | 3 |
| locations_count | 3 |
| best_oa_location.id | doi:10.1093/nar/gkz970 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S134668137 |
| best_oa_location.source.issn | 0305-1048, 1362-4954, 1362-4962 |
| best_oa_location.source.type | journal |
| best_oa_location.source.is_oa | True |
| best_oa_location.source.issn_l | 0305-1048 |
| best_oa_location.source.is_core | True |
| best_oa_location.source.is_in_doaj | True |
| best_oa_location.source.display_name | Nucleic Acids Research |
| best_oa_location.source.host_organization | https://openalex.org/P4310311648 |
| best_oa_location.source.host_organization_name | Oxford University Press |
| best_oa_location.source.host_organization_lineage | https://openalex.org/P4310311648, https://openalex.org/P4310311647 |
| best_oa_location.source.host_organization_lineage_names | Oxford University Press, University of Oxford |
| best_oa_location.license | |
| best_oa_location.pdf_url | https://academic.oup.com/nar/article-pdf/48/D1/D246/31697977/gkz970.pdf |
| best_oa_location.version | publishedVersion |
| best_oa_location.raw_type | journal-article |
| best_oa_location.license_id | |
| best_oa_location.is_accepted | True |
| best_oa_location.is_published | True |
| best_oa_location.raw_source_name | Nucleic Acids Research |
| best_oa_location.landing_page_url | https://doi.org/10.1093/nar/gkz970 |
| primary_location.id | doi:10.1093/nar/gkz970 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S134668137 |
| primary_location.source.issn | 0305-1048, 1362-4954, 1362-4962 |
| primary_location.source.type | journal |
| primary_location.source.is_oa | True |
| primary_location.source.issn_l | 0305-1048 |
| primary_location.source.is_core | True |
| primary_location.source.is_in_doaj | True |
| primary_location.source.display_name | Nucleic Acids Research |
| primary_location.source.host_organization | https://openalex.org/P4310311648 |
| primary_location.source.host_organization_name | Oxford University Press |
| primary_location.source.host_organization_lineage | https://openalex.org/P4310311648, https://openalex.org/P4310311647 |
| primary_location.source.host_organization_lineage_names | Oxford University Press, University of Oxford |
| primary_location.license | |
| primary_location.pdf_url | https://academic.oup.com/nar/article-pdf/48/D1/D246/31697977/gkz970.pdf |
| primary_location.version | publishedVersion |
| primary_location.raw_type | journal-article |
| primary_location.license_id | |
| primary_location.is_accepted | True |
| primary_location.is_published | True |
| primary_location.raw_source_name | Nucleic Acids Research |
| primary_location.landing_page_url | https://doi.org/10.1093/nar/gkz970 |
| publication_date | 2019-10-11 |
| publication_year | 2019 |
| referenced_works | https://openalex.org/W2149769193, https://openalex.org/W2102473929, https://openalex.org/W2041877620, https://openalex.org/W2158266834, https://openalex.org/W2166277117, https://openalex.org/W2168341872, https://openalex.org/W1963778673, https://openalex.org/W2099757081, https://openalex.org/W2034145535, https://openalex.org/W2167296922, https://openalex.org/W2012114217, https://openalex.org/W1990893875, https://openalex.org/W2587481461, https://openalex.org/W2087058596, https://openalex.org/W2012627860, https://openalex.org/W2166755632, https://openalex.org/W2155844132, https://openalex.org/W2417218538, https://openalex.org/W2002964220, https://openalex.org/W2950680707, https://openalex.org/W2951189885, https://openalex.org/W2910641511, https://openalex.org/W2064604026, https://openalex.org/W2069520341, https://openalex.org/W2769058621, https://openalex.org/W2760991039, https://openalex.org/W2509668036, https://openalex.org/W2625488274, https://openalex.org/W2610903912, https://openalex.org/W2078641190, https://openalex.org/W2766967795, https://openalex.org/W2770182290, https://openalex.org/W2128059998, https://openalex.org/W2401562190, https://openalex.org/W2041686632, https://openalex.org/W2163964975, https://openalex.org/W2792170325, https://openalex.org/W1984521378, https://openalex.org/W2770001620, https://openalex.org/W2022736304, https://openalex.org/W2807228729, https://openalex.org/W2227516629, https://openalex.org/W2988716798, https://openalex.org/W2116467413, https://openalex.org/W2268267797, https://openalex.org/W2063195483, https://openalex.org/W2122199548, https://openalex.org/W2007071268, https://openalex.org/W2092454365, https://openalex.org/W2036681286, https://openalex.org/W2794294274, https://openalex.org/W2021534482, https://openalex.org/W2804344327, https://openalex.org/W2744040456, https://openalex.org/W2059099579, https://openalex.org/W2157458089, https://openalex.org/W2134349183, https://openalex.org/W2049888367, https://openalex.org/W2951699110, https://openalex.org/W2899379544 |
| referenced_works_count | 60 |
| abstract_inverted_index.a | 4, 73 |
| abstract_inverted_index.13 | 149 |
| abstract_inverted_index.39 | 137 |
| abstract_inverted_index.We | 41, 167 |
| abstract_inverted_index.be | 25 |
| abstract_inverted_index.in | 31, 51, 54, 110, 117, 200 |
| abstract_inverted_index.is | 3, 23 |
| abstract_inverted_index.of | 11, 47, 66, 96, 177, 190 |
| abstract_inverted_index.to | 24, 27, 53, 60, 82, 129, 183, 194 |
| abstract_inverted_index.DNA | 159, 196 |
| abstract_inverted_index.TFs | 135, 191 |
| abstract_inverted_index.The | 17, 85, 140 |
| abstract_inverted_index.and | 45, 57, 71, 75, 103, 116, 152, 160, 171, 179, 186, 192 |
| abstract_inverted_index.for | 7, 20, 79, 133, 143, 157, 164, 173 |
| abstract_inverted_index.has | 127 |
| abstract_inverted_index.its | 69 |
| abstract_inverted_index.new | 64, 89, 181 |
| abstract_inverted_index.now | 147 |
| abstract_inverted_index.the | 43, 83, 92, 101, 122, 169, 174 |
| abstract_inverted_index.web | 77 |
| abstract_inverted_index.1900 | 134 |
| abstract_inverted_index.2428 | 130 |
| abstract_inverted_index.DNA. | 62, 166 |
| abstract_inverted_index.TFBS | 145 |
| abstract_inverted_index.This | 63 |
| abstract_inverted_index.able | 26 |
| abstract_inverted_index.data | 37 |
| abstract_inverted_index.each | 144 |
| abstract_inverted_index.easy | 80 |
| abstract_inverted_index.four | 161 |
| abstract_inverted_index.from | 35, 49, 58, 91, 100, 109, 121, 136 |
| abstract_inverted_index.main | 18 |
| abstract_inverted_index.most | 93 |
| abstract_inverted_index.this | 21 |
| abstract_inverted_index.vivo | 55, 118 |
| abstract_inverted_index.(TFs) | 99 |
| abstract_inverted_index.TFBSs | 107, 120, 178 |
| abstract_inverted_index.data. | 84 |
| abstract_inverted_index.entry | 146 |
| abstract_inverted_index.minor | 153 |
| abstract_inverted_index.modes | 34 |
| abstract_inverted_index.motif | 5 |
| abstract_inverted_index.shape | 150, 162 |
| abstract_inverted_index.sites | 15 |
| abstract_inverted_index.tools | 182 |
| abstract_inverted_index.vitro | 52, 111 |
| abstract_inverted_index.JASPAR | 102 |
| abstract_inverted_index.TFBSs. | 201 |
| abstract_inverted_index.access | 81 |
| abstract_inverted_index.assays | 115 |
| abstract_inverted_index.derive | 28, 195 |
| abstract_inverted_index.factor | 13 |
| abstract_inverted_index.groove | 154 |
| abstract_inverted_index.mostly | 50 |
| abstract_inverted_index.recent | 94 |
| abstract_inverted_index.binding | 14, 56, 114 |
| abstract_inverted_index.compare | 184 |
| abstract_inverted_index.content | 126 |
| abstract_inverted_index.current | 86 |
| abstract_inverted_index.derived | 108 |
| abstract_inverted_index.entries | 90 |
| abstract_inverted_index.factors | 98 |
| abstract_inverted_index.include | 148 |
| abstract_inverted_index.methods | 193 |
| abstract_inverted_index.readout | 33 |
| abstract_inverted_index.release | 65 |
| abstract_inverted_index.without | 38 |
| abstract_inverted_index.(TFBSs). | 16 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.UniPROBE | 104 |
| abstract_inverted_index.accuracy | 172 |
| abstract_inverted_index.database | 6, 22 |
| abstract_inverted_index.designed | 180 |
| abstract_inverted_index.extended | 42 |
| abstract_inverted_index.features | 151, 163 |
| abstract_inverted_index.improved | 168 |
| abstract_inverted_index.improves | 68 |
| abstract_inverted_index.includes | 88 |
| abstract_inverted_index.insights | 30 |
| abstract_inverted_index.launches | 72 |
| abstract_inverted_index.profiles | 10, 132, 142, 189 |
| abstract_inverted_index.quantity | 44 |
| abstract_inverted_index.species. | 139 |
| abstract_inverted_index.standard | 158 |
| abstract_inverted_index.TFBSshape | 1, 67, 125 |
| abstract_inverted_index.alignment | 176 |
| abstract_inverted_index.analyzing | 8 |
| abstract_inverted_index.available | 39 |
| abstract_inverted_index.database. | 124 |
| abstract_inverted_index.different | 138 |
| abstract_inverted_index.expansion | 87 |
| abstract_inverted_index.increased | 128 |
| abstract_inverted_index.interface | 78 |
| abstract_inverted_index.mutations | 199 |
| abstract_inverted_index.potential | 156 |
| abstract_inverted_index.rationale | 19 |
| abstract_inverted_index.MeDReaders | 123 |
| abstract_inverted_index.TFBSshape, | 48 |
| abstract_inverted_index.databases, | 105 |
| abstract_inverted_index.methylated | 61, 106, 119, 165, 185 |
| abstract_inverted_index.nucleotide | 198 |
| abstract_inverted_index.responsive | 74 |
| abstract_inverted_index.sequencing | 36 |
| abstract_inverted_index.structural | 9, 131, 141, 188 |
| abstract_inverted_index.collections | 95 |
| abstract_inverted_index.flexibility | 170 |
| abstract_inverted_index.mechanistic | 29 |
| abstract_inverted_index.shape-based | 175 |
| abstract_inverted_index.structures. | 40 |
| abstract_inverted_index.EpiSELEX-seq | 113 |
| abstract_inverted_index.unmethylated | 59, 187 |
| abstract_inverted_index.electrostatic | 155 |
| abstract_inverted_index.functionality | 70 |
| abstract_inverted_index.protein–DNA | 32 |
| abstract_inverted_index.transcription | 12, 97 |
| abstract_inverted_index.user-friendly | 76 |
| abstract_inverted_index.dimensionality | 46 |
| abstract_inverted_index.high-throughput | 112 |
| abstract_inverted_index.shape-preserving | 197 |
| abstract_inverted_index.(https://tfbsshape.usc.edu) | 2 |
| cited_by_percentile_year.max | 99 |
| cited_by_percentile_year.min | 96 |
| corresponding_author_ids | https://openalex.org/A5019996279 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 5 |
| corresponding_institution_ids | https://openalex.org/I1174212 |
| citation_normalized_percentile.value | 0.89257541 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |