Evidence map›Paper›PMID 36672963›Full record

ArticleGenes2023

Evolutionary Landscape of

Adam Underwood, Daniel T Rasicci, David Hinds, Jackson T Mitchell, Jacob K Zieba, Joshua Mills, Nicholas E Arnold, Taylor W Cook, Mehdi Moustaqil, Yann Gambin and 22 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
2.8field-weighted citation impact, top 9% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 9 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. Review
  5. Review
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

32 authors at 11 institutions in 3 countries.

Adam UnderwoodDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.ORCID 0000-0001-8232-4129
Daniel T RasicciDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
David HindsHudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
Jackson T MitchellDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
Jacob K ZiebaDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.ORCID 0000-0003-4163-6569
Joshua MillsDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
Nicholas E ArnoldDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
Taylor W CookDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
Mehdi MoustaqilSingle Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia.
Yann GambinSingle Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia.
Emma SiereckiSingle Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia.ORCID 0000-0001-9970-868X
Frank FontaineInstitute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
Sophie VanderweeleDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.ORCID 0000-0001-7368-6128
Akansha S DasDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
William CvammenDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.ORCID 0000-0002-6417-905X
Olivia SirpillaDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
Xavier SoehnlenDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
Kristen BrickerDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
Maram AlokailiDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
Morgan GreenDepartment of Chemistry, Grand Valley State University, Allendale, MI 49401, USA.
Sadie HeeringaDepartment of Biology, Calvin University, Grand Rapids, MI 49546, USA.
Amy M WilstermannDepartment of Biology, Calvin University, Grand Rapids, MI 49546, USA.
Thomas M FreelandDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
Dinah QutobDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
Amy MilstedDivision of Mathematics and Science, Walsh University, North Canton, OH 44720, USA.
Ralf JauchSchool of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 518057, China.ORCID 0000-0002-6590-9579
Timothy J TricheCenter for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
Connie M KrawczykDepartment of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA.ORCID 0000-0002-2468-5986
Caleb P BuppDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.ORCID 0000-0003-4255-0396
Surender RajasekaranDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
Mathias FrancoisThe Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Sydney, NSW 2006, Australia.
Jeremy W ProkopDepartment of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA.
Walsh University · USMichigan State University · USSpectrum Health · USUNSW Sydney · AUCalvin University · USVan Andel Institute · USChinese University of Hong Kong · HKGrand Valley State University · USHudsonAlpha Institute for Biotechnology · USThe University of Queensland · AUThe University of Sydney · AU

Funding

The roles of genetics, hormones, and gender in sexually dimorphic immune responseR01AI171984 · NIAID · VAN ANDEL RESEARCH INSTITUTE · PI KRAWCZYK, CONNIE, PROKOP, JEREMY WILLIAM · 2022 to 2024
$1.4M
Using a Sequence-to-Structure-to-Function Approach to Functionally Characterize Protein Coding Missense Mutations in the Human and Rat GenomesK01ES025435 · NIEHS · MICHIGAN STATE UNIVERSITY · PI PROKOP, JEREMY WILLIAM · 2014 to 2018
$489k
NIAID NIH HHS R01 AI171984NIEHS NIH HHS K01 ES025435
6 · The paper itself

Abstract

The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.

Indexed as

High Mobility Group ProteinsSOX Transcription FactorsAmino Acid SequenceDimerizationGenotypeHumansSOXB2 Transcription FactorsSOXE Transcription FactorsSOXF Transcription FactorsHigh Mobility Group ProteinsSOX14 protein, humanSOX18 protein, humanSOX7 protein, humanSOX8 protein, humanSOXB2 Transcription FactorsSOXE Transcription FactorsSOXF Transcription FactorsSOX Transcription Factorsdevelopmental biologyparalog mappingSOX genestranscription factorvariant data integration

Identifiers

PMID36672963
PMCPMC9859272
OpenAlexW4316464584

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.