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Protocols

ORTI specifications

Information


Unique identifier OMICS_24634
Name ORTI
Alternative name Open-access Repository of Transcriptional Interactions
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Maintainer


  • person_outline Fatemeh Vafaee

Publication for Open-access Repository of Transcriptional Interactions

ORTI citations

 (6)
call_split

Topological congruence between phylogenies of Anacanthorus spp. (Monogenea: Dactylogyridae) and their Characiformes (Actinopterygii) hosts: A case of host parasite cospeciation

2018
PLoS One
PMCID: 5851586
PMID: 29538463
DOI: 10.1371/journal.pone.0193408
call_split See protocol

[…] inutes at 72°C. The nuclear RAG1 gene of S. marginatus was amplified with primers RAG1-4063R (5´- TTCTGNARRTACTTGGARGTGTAWAGCCA-3´) and RAG1-3098F (5´- TGTGCCTGATGYTYGTDGAYGART-3´) designed by Li and Ortí []. The amplification conditions were in 41 cycles, with denaturation at 94°C for 4 minutes in the first cycle and 15 seconds in the rest, annealing at 55°C for 30 seconds, extension for 2 minute […]

library_books

The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes

2018
Sci Rep
PMCID: 5789081
PMID: 29379070
DOI: 10.1038/s41598-018-20104-x

[…] originally developed for analysing phosphoproteomics data) to gene expression data and for identifying TF-TG interactions and TF signalling events. To achieve this, we used TF-TG annotations from the ORTI database as the knowledge-base to evaluate the clusters instead of the default kinase substrate relationships.We also adapted the clueR package to incorporate hierarchical clustering (HC). This e […]

library_books

Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper

2017
Ecol Evol
PMCID: 5773313
PMID: 29375806
DOI: 10.1002/ece3.3745

[…] amino acids states at each ancestral nodes were inferred based on their inferred likelihood. The initial tree was inferred from morphological phylogeny (Nelson, ) and molecular phylogeny (Betancur & Orti, ). The rates among sites were treated as uniform among sites. The analysis involved eight amino acid sequences. Evolutionary analyses were conducted in MEGA5 (Tamura et al., ). […]

call_split

Reversed brain size sexual dimorphism accompanies loss of parental care in white sticklebacks

2014
Ecol Evol
PMCID: 4222210
PMID: 25473476
DOI: 10.1002/ece3.1175
call_split See protocol

[…] (Jombart ). We did not analyze the relationship between Pacific and Atlantic sticklebacks – however, they are estimated to have been isolated from the Atlantic populations for 90–260 thousand years (Orti et al. ). […]

library_books

The Tree of Life and a New Classification of Bony Fishes

2013
PLoS Curr
PMCID: 3644299
PMID: 23653398
DOI: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288

[…] l.), Diplophidae (following Nelson; apparently omitted by Eschmeyer and Fong), Horabagridae (following Sullivan et al.), Sinipercidae (following Li et al.), Steindachneriidae (following Roa-Varon and Ortí), Zanclorhynchidae, the aulopiform Bathysauropsidae and Sudidae (following Davis), and the pleuronectiform Paralichthodidae, Poecilopsettidae, and Rhombosoleidae (following Chapleau, Munroe, Beta […]

library_books

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

2011
BMC Evol Biol
PMCID: 3141434
PMID: 21693066
DOI: 10.1186/1471-2148-11-177

[…] osely related to Siluriformes (BSP = 52%) than to Citharinoidei.Paraphyletic characiforms have been repeatedly recovered in previous molecular studies (Figure ) but in different manners. For example, Ortí and Meyer [] assembled nuclear ependymin sequences (588 bp) from 22 otophysans to explore the phylogenetic utility of this gene and found that characoids were more closely related to Gymnotiforme […]


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ORTI institution(s)
Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia; Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia; School of Physics, The University of Sydney, Sydney, NSW, Australia
ORTI funding source(s)
Supported by a grant from the National Health and Medical Research Council (NHMRC; GNT1061122), an NHMRC Senior Research Fellow (APP1019680), an NHMRC Early Career Fellowship (APP1072440) and a Judith and David Coffey Gif.

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