CoChat
Sign Up
Cited by 16

The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.

Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals

Berger, Mark J, Wenger, Aaron M, Guturu, Harendra, Bejerano, Gill·2018·Nucleic Acids Research
DOI 10.1093/nar/gky741PMC PMC6182171

Published version of a preprint

Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gky741

Cites

5 of 5 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 56

  1. Monod, 1961, Teleonomic mechanisms in cellular metabolism, growth, and differentiation, Cold Spring Harb. Symp. Quant. Biol., 26, 389, 10.1101/SQB.1961.026.01.048 · DOI
  2. King, 1975, Evolution at two levels in humans and chimpanzees, Science, 188, 107, 10.1126/science.1090005 · DOI · Paper page
  3. Carroll, 2008, Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution, Cell, 134, 25, 10.1016/j.cell.2008.06.030 · DOI · Paper page
  4. Hoekstra, 2007, The locus of evolution: evo devo and the genetics of adaptation, Evolution, 61, 995, 10.1111/j.1558-5646.2007.00105.x · DOI
  5. Shapiro, 2004, Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks, Nature, 428, 717, 10.1038/nature02415 · DOI
  6. Michelson, 2002, Deciphering genetic regulatory codes: a challenge for functional genomics, Proc. Natl. Acad. Sci. U.S.A., 99, 546, 10.1073/pnas.032685999 · DOI
  7. Bradley, 2010, Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species, PLoS Biol., 8, e1000343, 10.1371/journal.pbio.1000343 · DOI
  8. Schmidt, 2010, Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding, Science, 328, 1036, 10.1126/science.1186176 · DOI · Paper page
  9. Ballester, 2014, Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways, eLife, 3, e02626, 10.7554/eLife.02626 · DOI · Paper page
  10. Arbiza, 2013, Genome-wide inference of natural selection on human transcription factor binding sites, Nat. Genet., 45, 723, 10.1038/ng.2658 · DOI
  11. Villar, 2015, Enhancer evolution across 20 mammalian species, Cell, 160, 554, 10.1016/j.cell.2015.01.006 · DOI · Paper page
  12. Kvon, 2016, Progressive loss of function in a limb enhancer during snake evolution, Cell, 167, 633, 10.1016/j.cell.2016.09.028 · DOI
  13. Marcovitz, 2016, ‘Reverse Genomics’ predicts function of human conserved noncoding elements, Mol. Biol. Evol., 33, 1358, 10.1093/molbev/msw001 · DOI · Paper page
  14. Hiller, 2012, A ‘forward genomics’ approach links genotype to phenotype using independent phenotypic losses among related species, Cell Rep., 2, 817, 10.1016/j.celrep.2012.08.032 · DOI · Paper page
  15. Finger, 2017, The mouse Gene Expression Database (GXD): 2017 update, Nucleic Acids Res., 45, D730, 10.1093/nar/gkw1073 · DOI
  16. Kent, 2002, The Human Genome Browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102 · DOI · Paper page
  17. Guturu, 2016, Erosion of conserved binding sites in personal genomes points to medical histories, PLoS Comput. Biol., 12, e1004711, 10.1371/journal.pcbi.1004711 · DOI
  18. Guturu, 2013, Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements, Philos. Trans. R. Soc. Lond. B. Biol. Sci., 368, 20130029, 10.1098/rstb.2013.0029 · DOI
  19. Jolma, 2013, DNA-binding specificities of human transcription factors, Cell, 152, 327, 10.1016/j.cell.2012.12.009 · DOI
  20. Wenger, 2013, PRISM offers a comprehensive genomic approach to transcription factor function prediction, Genome Res., 23, 889, 10.1101/gr.139071.112 · DOI
  21. Kel, 2003, MATCH: a tool for searching transcription factor binding sites in DNA sequences, Nucleic Acids Res., 31, 3576, 10.1093/nar/gkg585 · DOI
  22. Xie, 2009, MotifMap: a human genome-wide map of candidate regulatory motif sites, Bioinformatics, 25, 167, 10.1093/bioinformatics/btn605 · DOI
  23. ENCODE Project Consortium, 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 · DOI · Paper page
  24. Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 · DOI · Paper page
  25. Phipson, 2010, Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn, Stat. Appl. Genet. Mol. Biol., 9, Article 39, 10.2202/1544-6115.1585 · DOI · Paper page
  26. McLean, 2010, GREAT improves functional interpretation of cis-regulatory regions, Nat. Biotechnol., 28, 495, 10.1038/nbt.1630 · DOI · Paper page
  27. Foote, 2015, Convergent evolution of the genomes of marine mammals, Nat. Genet., 47, 272, 10.1038/ng.3198 · DOI
  28. Newburger, 2009, UniPROBE: an online database of protein binding microarray data on protein–DNA interactions, Nucleic Acids Res., 37, D77, 10.1093/nar/gkn660 · DOI
  29. Bryne, 2008, JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update, Nucleic Acids Res., 36, D102, 10.1093/nar/gkm955 · DOI
  30. Matys, 2006, TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes, Nucleic Acids Res., 34, D108, 10.1093/nar/gkj143 · DOI
  31. Don, 2013, The evolutionary history of the development of the pelvic fin/hindlimb, J. Anat., 222, 114, 10.1111/j.1469-7580.2012.01557.x · DOI
  32. Don, 2011, Morphology of pelvic fin loss in a zebrafish strain (Danio rerio), J. Morphol., 272, 583, 10.1002/jmor.10938 · DOI
  33. Fish, 1994, Influence of hydrodynamic-design and propulsive mode on mammalian swimming energetics, Aust. J. Zool., 42, 79, 10.1071/ZO9940079 · DOI
  34. Visel, 2007, VISTA Enhancer Browser—a database of tissue-specific human enhancers, Nucleic Acids Res., 35, D88, 10.1093/nar/gkl822 · DOI · Paper page
  35. Emerling, 2014, Eyes underground: regression of visual protein networks in subterranean mammals, Mol. Phylogenet. Evol., 78, 260, 10.1016/j.ympev.2014.05.016 · DOI
  36. Prudent, 2016, Controlling for phylogenetic relatedness and evolutionary rates improves the discovery of associations between species’ phenotypic and genomic differences, Mol. Biol. Evol., 33, 2135, 10.1093/molbev/msw098 · DOI · Paper page
  37. Crish, 2006, Central visual system of the naked mole-rat (Heterocephalus glaber), Anat. Rec. A. Discov. Mol. Cell. Evol. Biol., 288, 205, 10.1002/ar.a.20288 · DOI
  38. Crish, 2003, Somatosensation in the superior colliculus of the star-nosed mole, J. Comp. Neurol., 464, 415, 10.1002/cne.10791 · DOI
  39. McNAB, 1970, Body weight and the energetics of temperature regulation, J. Exp. Biol., 53, 329, 10.1242/jeb.53.2.329 · DOI
  40. Allbrook, 1958, Temperature regulation in the white rhinoceros, J. Physiol., 143, 51
  41. Khamas, 2012, Skin histology and its role in heat dissipation in three pinniped species, Acta Vet. Scand., 54, 46, 10.1186/1751-0147-54-46 · DOI
  42. Pescovitz, 2004, Pediatric Endocrinology: Mechanisms, Manifestations, and Management
  43. Kleisner, 2010, The evolutionary history of testicular externalization and the origin of the scrotum, J. Biosci., 35, 27, 10.1007/s12038-010-0005-7 · DOI
  44. Sharma, 2018, Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals, PLoS Biol., 16, e2005293, 10.1371/journal.pbio.2005293 · DOI
  45. Hampton, 1971, Heat transfer and body temperature in the Atlantic bottlenose dolphin, Tursiops truncatus, Int. J. Biometeorol., 15, 247, 10.1007/BF01803907 · DOI
  46. Joseph, 2009, Development and morphogenesis of the Wolffian/epididymal duct, more twists and turns, Dev. Biol., 325, 6, 10.1016/j.ydbio.2008.10.012 · DOI
  47. Yang, 2010, Common SNPs explain a large proportion of the heritability for human height, Nat. Genet., 42, 565, 10.1038/ng.608 · DOI · Paper page
  48. Marcil, 2003, Pitx1 and Pitx2 are required for development of hindlimb buds, Development, 130, 45, 10.1242/dev.00192 · DOI
  49. Chen, 1998, Limb and kidney defects in Lmx1b mutant mice suggest an involvement of LMX1B in human nail patella syndrome, Nat. Genet., 19, 51, 10.1038/ng0598-51 · DOI
  50. Vogel, 1995, Dorsal cell fate specified by chick Lmx1 during vertebrate limb development, Nature, 378, 716, 10.1038/378716a0 · DOI
  51. Torres, 1996, Pax2 contributes to inner ear patterning and optic nerve trajectory, Development, 122, 3381, 10.1242/dev.122.11.3381 · DOI
  52. Fantin, 2014, Neuropilin 1 (NRP1) hypomorphism combined with defective VEGF-A binding reveals novel roles for NRP1 in developmental and pathological angiogenesis, Development, 141, 556, 10.1242/dev.103028 · DOI
  53. Kaftanovskaya, 2013, Left-sided cryptorchidism in mice with Wilms’ tumour 1 gene deletion in gubernaculum testis, J. Pathol., 230, 39, 10.1002/path.4161 · DOI
  54. Brand-Saberi, 2002, Vertebrate Myogenesis, 10.1007/978-3-540-45686-5 · DOI
  55. Lerner, 2005, Sp4 is expressed in retinal neurons, activates transcription of photoreceptor-specific genes, and synergizes with Crx, J. Biol. Chem., 280, 20642, 10.1074/jbc.M500957200 · DOI
  56. Schimmenti, 2011, Renal coloboma syndrome, Eur. J. Hum. Genet., 19, 1207, 10.1038/ejhg.2011.102 · DOI

Cited by

Sorted by citations

Metadata

Authors
Berger, M. J., Wenger, A. M., Guturu, H., & Bejerano, G.
Affiliations
  • Department of Computer Science, Stanford University, Stanford, CA 94305-5329, USA
  • Department of Electrical Engineering, Stanford University, Stanford, CA 94305-5008, USA
ORCID
Bejerano, Gill
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2018-08-23
Volume
46
Issue
18
Pages
9299-9308
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gky741
PMC
PMC6182171
Cited by
16
References
5
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • National Science Foundation (DGE-1656518)
  • National Institutes of Health (U01MH105949, R01HG008742)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review