cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/kpe7n5
title: Automated recognition of brain region mentions in neuroscience literature

description: The ability to computationally extract mentions of neuroanatomical regions from the literature would assist linking to other entities within and outside of an article. Examples include extracting reports of connectivity or region-specific gene expression. To facilitate text mining of neuroscience literature we have created a corpus of manually annotated brain region mentions. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. The corpus is freely available at http://www.chibi.ubc.ca/WhiteText/.
DOI: 10.5683/sp2/qw7or9
title: A methodology for the analysis of differential coexpression across the human lifespan

description: BACKGROUND: Differential coexpression is a change in coexpression between genes that may reflect 'rewiring' of transcriptional networks. It has previously been hypothesized that such changes might be occurring over time in the lifespan of an organism. While both coexpression and differential expression of genes have been previously studied in life stage change or aging, differential coexpression has not. Generalizing differential coexpression analysis to many time points presents a methodological challenge. Here we introduce a method for analyzing changes in coexpression across multiple ordered groups (e.g., over time) and extensively test its validity and usefulness. RESULTS: Our method is based on the use of the Haar basis set to efficiently represent changes in coexpression at multiple time scales, and thus represents a principled and generalizable extension of the idea of differential coexpression to life stage data. We used published microarray studies categorized by age to test the methodology. We validated the methodology by testing our ability to reconstruct Gene Ontology (GO) categories using our measure of differential coexpression and compared this result to using coexpression alone. Our method allows significant improvement in characterizing these groups of genes. Further, we examine the statistical properties of our measure of differential coexpression and establish that the results are significant both statistically and by an improvement in semantic similarity. In addition, we found that our method finds more significant changes in gene relationships compared to several other methods of expressing temporal relationships between genes, such as coexpression over time. CONCLUSION: Differential coexpression over age generates significant and biologically relevant information about the genes producing it. Our Haar basis methodology for determining age-related differential coexpression performs better than other tested methods. The Haar basis set also lends itself to ready interpretation in terms of both evolutionary and physiological mechanisms of aging and can be seen as a natural generalization of two-category differential coexpression. CONTACT: paul@bioinformatics.ubc.ca.
DOI: 10.5683/sp2/5x4gvz
title: Systematic evaluation of isoform function in literature reports of alternative splicing

description: Systematic evaluation of splice isoform function to determine genes with functionally distinct splice isoforms based on experimental evidence. Framework and analysis of curation provided in the above preprint. The data are provided in two parts. First part is the PubMed IDs of all curated studies and their annotations based on our curation framework. Second, are the genes with literature evidence of functionally distinct splice isoforms, and further notes about functional distinctness.
DOI: 10.5683/sp2/nvboaz
title: Application and evaluation of automated semantic annotation of gene expression experiments

description: MOTIVATION: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets. RESULTS: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma. AVAILABILITY: The source code, documentation and Supplementary Materials are available at http://www.chibi.ubc.ca/GEOMMTX. The results of the manual evaluations are provided as Supplementary Material. Both manual and predicted annotations can be viewed and searched via the Gemma website at http://www.chibi.ubc.ca/Gemma. The complete set of predicted annotations is available as a machine readable resource description framework graph.
DOI: 10.5683/sp2/qaimtk
title: Sharing and reusing gene expression profiling data in neuroscience

description: As public availability of gene expression profiling data increases, it is natural to ask how these data can be used by neuroscientists. Here we review the public availability of high-throughput expression data in neuroscience and how it has been reused, and tools that have been developed to facilitate reuse. There is increasing interest in making expression data reuse a routine part of the neuroscience tool-kit, but there are a number of challenges. Data must become more readily available in public databases; efforts to encourage investigators to make data available are important, as is education on the benefits of public data release. Once released, data must be better-annotated. Techniques and tools for data reuse are also in need of improvement. Integration of expression profiling data with neuroscience-specific resources such as anatomical atlases will further increase the value of expression data.
DOI: 10.5683/sp2/madffc
title: Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms

description: The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here, we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms.
DOI: 10.5683/sp2/jojyop
title: Coexpression Analysis of Human Genes Across Many Microarray Data Sets

description: We present a large-scale analysis of mRNA coexpression based on 60 large human data sets containing a total of 3924 microarrays. We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in multiple data sets, establishing a high-confidence network of 8805 genes connected by 220,649 “coexpression links” that are observed in at least three data sets. Confirmed positive correlations between genes were much more common than confirmed negative correlations. We show that confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes. Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function.
DOI: 10.5683/sp2/ytdepn
title: Altered Hippocampal Transcript Profile Accompanies an Age-Related Spatial Memory Deficit in Mice

description: We have carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze. By using Affymetrix GeneChip microarrays, we found a distinct pattern of age-related change, consisting mostly of gene overexpression in the middle-aged mice, suggesting that the induction of negative regulators in the middle-aged hippocampus could be involved in impairment of learning. Interestingly, we report changes in transcript levels for genes that could affect synaptic plasticity. Those changes could be involved in the memory deficits we observed in the 15-month-old mice. In agreement with previous reports, we also found altered expression in genes related to inflammation, protein processing, and oxidative stress.
DOI: 10.5683/sp2/eyesm1
title: The effect of replication on gene expression microarray experiments

description: MOTIVATION: We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication. RESULTS: While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used. Conversely, for most studies, 10-15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.
DOI: 10.5683/sp2/qcleij
title: Using ANOVA for gene selection from microarray studies of the nervous system

description: Methods are presented for detecting differential expression using statistical hypothesis testing methods including analysis of variance (ANOVA). Practicalities of experimental design, power, and sample size are discussed. Methods for multiple testing correction and their application are described. Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/.
DOI: 10.5683/sp2/gpwpkx
title: Analysis of strain and regional variation in gene expression in mouse brain

description: BACKGROUND: We performed a statistical analysis of a previously published set of gene expression microarray data from six different brain regions in two mouse strains. In the previous analysis, 24 genes showing expression differences between the strains and about 240 genes with regional differences in expression were identified. Like many gene expression studies, that analysis relied primarily on ad hoc 'fold change' and 'absent/present' criteria to select genes. To determine whether statistically motivated methods would give a more sensitive and selective analysis of gene expression patterns in the brain, we decided to use analysis of variance (ANOVA) and feature selection methods designed to select genes showing strain- or region-dependent patterns of expression. RESULTS: Our analysis revealed many additional genes that might be involved in behavioral differences between the two mouse strains and functional differences between the six brain regions. Using conservative statistical criteria, we identified at least 63 genes showing strain variation and approximately 600 genes showing regional variation. Unlike ad hoc methods, ours have the additional benefit of ranking the genes by statistical score, permitting further analysis to focus on the most significant. Comparison of our results to the previous studies and to published reports on individual genes show that we achieved high sensitivity while preserving selectivity. CONCLUSIONS: Our results indicate that molecular differences between the strains and regions studied are larger than indicated previously. We conclude that for large complex datasets, ANOVA and feature selection, alone or in combination, are more powerful than methods based on fold-change thresholds and other ad hoc selection criteria.
DOI: 10.5683/sp2/cfcjpy
title: Meta-analysis of kindling-induced gene expression changes in the rat hippocampus

description: Numerous studies have been performed to examine gene expression patterns in the rodent hippocampus in the kindling model of epilepsy. However, recent reviews of this literature have revealed limited agreement among studies. Because this conclusion was based on retrospective comparison of reported "hit lists" from individual studies, we hypothesized that re-analysis of the original expression data would help address this concern. In this paper, we reanalyzed four genome-wide expression studies of excitotoxin-induced kindling in rat and performed a statistical meta-analysis. The meta-analysis revealed over 800 genes which show significant change in expression 24 h after initial seizure induction, and 59 genes altered after 10 days. To evaluate our results in light of previous work, we assembled a reference list of genes formed from a consensus of the published literature. Our profiles include most of the genes in this reference list, and most of the additional genes are from pathways or biological processes previously recognized to be altered in kindling. In addition our results emphasized expression changes in lipid metabolism and protein degradation pathways. We conclude that a cautious re-analysis of published expression data can help illuminate genes and pathways underling kindling. Supplementary Material is available at http://www.chibi.ubc.ca/faculty/pavlidis/meta-analysis-of-brain-kindling/.
DOI: 10.5683/sp2/fjwil8
title: Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation

description: Supporting data for "Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation"
DOI: 10.5683/sp2/dqokpb
title: Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction

description: Supporting data for "Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction"
DOI: 10.5683/sp2/xllwrl
title: Experiment level curation identifies high confidence transcriptional regulatory interactions in neurodevelopment

description: The capacity to computationally reconstruct gene regulatory networks using large-scale biological data is currently limited by the absence of a high confidence set of one-to-one regulatory interactions. Given the lengthy history of using small scale experimental assays to investigate individual interactions, we hypothesize that a reliable collection of gene regulatory interactions could be compiled by systematically inspecting the published literature. To this end, we developed a curation protocol to examine and record evidence of regulatory interactions at the individual experiment level. Focusing on the area of brain development, we applied our pipeline to 1,310 publications. We identified 3,601 individual experiments, providing detailed information about 1,499 regulatory interactions. Many of these interactions have verified activity specifically in the embryonic brain. By capturing reports of regulatory interactions at this level of granularity, we present a resource that is more interpretable than other similar resources. List of Tables in TSV format: Supplementary Table S1. List of candidate papers Supplementary Table S2. List of TFs Supplementary Table S3. Curated records at the experiment level Supplementary Table S4. Curated records summarized at the DTRI level Supplementary Table S5. TF Perturbation experiment details Supplementary Table S6. TF-DNA Binding experiment details Supplementary Table S7. TF-reporter experiment details Supplementary Table S8. All DTRI records including those curated in external databases Supplementary Table S9. Records obtained from external databases Supplementary Table S10. List of differentially expressed genes following Pax6 perturbation Supplementary Table S11. Experiments with negative results
DOI: 10.5683/sp2/be6aea
title: LIST: Deleteriousness Levels of Amino Acid Variations

description: Predicting the Deleteriousness Level of for all possible Amino Acid variations in the human ~20K Swiss-Prot proteins. These predictions are entirely based on the Local Identity around mutation locations and the Shared Taxonomy between human and other species.
DOI: 10.5683/sp2/3ou15o
title: Figures data

description: Data for figures in nature communications
DOI: 10.5683/sp2/09y9ij
title: Type 2 Innate Lymphocytes are Crucial for Anti-tumour Immunity and Their Adoptive Transfer is an Effective Immunotherapy Against Cancer

description: Type 2 innate lymphoid cells (ILC2) potentiate adaptive immune responses however whether they have a role in mediating cancer immunity has not been assessed. Here, we report that mice genetically lacking ILC2s have significantly increased tumour growth rates and higher frequency of circulating tumour cells (CTCs) and metastasis to distal organs. Our data supports the conclusions that tumour-infiltrating ILC2s help mediate tumour immune-surveillance by promoting adaptive T cells responses and that ILC2s play a hitherto undescribed role in controlling metastasis. Furthermore, we demonstrate that adoptive transfer of ILC2s mediates a dramatic regression in cancer growth. Therefore, the adoptive transfer of ILC2s provides a new immunotherapeutic approach with the potential to aid in the eradication of cancers.
DOI: 10.5683/sp2/hfaa3v
title: PCP-SILAC

description: PCP-SILAC, scripts, instructions and sample data for informatics treatment of PCP-SILAC data.
DOI: 10.5683/sp2/v7ow8t
title: finalList

description: A tool that takes as input a non-redundant list of peptides identified in a project and compiles a non-redundant list of proteins identified. It will also subtract any peptides coming from a FASTA library of contaminants.
DOI: 10.5683/sp2/5qdkll
title: transORF

description: A tool that takes a FASTA nucleotide file and predicts all open reading frames in all six translation frames. The output is a FASTA amino acid file. This tool is useful for creating a protein library for database searching (where a good prediction is unavailable) if you don’t want to (or can’t) search your MS/MS spectra against a nucleotide library.
DOI: 10.5683/sp2/uvv4a0
title: JProteomics2014

description: Development of a computation framework for the analysis of protein correlation profiling and spatial proteomics experiments 2014
DOI: 10.5683/sp2/ndw1ww
title: Attachments to paper Scott et al Molecular System Biology (2017)

description: Attachments to paper Scott et al Molecular System Biology (2017)
DOI: 10.5683/sp2/3dkyyc
title: UBC Library Public Service Interactions Reported in Desk Tracker

description: UBC Library uses Desk Tracker software to record staff interactions with library patrons. Interactions are classified by type based on the nature of question and the effort and expertise required to respond. The question types used in this dataset can be mapped to the Association of Research Libraries' (ARL) definitions for reference and directional interactions: Reference (Basic, Intermediate, Advanced, and Comprehensive interaction types): "an information contact that involves the knowledge, use, recommendations, interpretation, or instruction in the use of one or more information sources by a member of the library staff." Directional (Hardware/authentication and Directional interaction types): "an information contact that facilitates the logistical use of the library and that does not involve the knowledge, use, recommendations, interpretation, or instruction in the use or creation of information sources other than those that describe the library, such as schedules, floor plans, and handbooks." Please contact Jeremy Buhler at jeremy.buhler@ubc.ca if you have questions.
DOI: 10.5683/sp2/ssbzfz
title: UBC Library Space Use Observation Study

description: During the sample week (Mar 31-Apr 6 2014) UBC Library staff counted the number of users in publicly available study space in the two largest UBC Vancouver library branches, Irving K. Barber Learning Centre and Koerner Library. Counts took place twice daily, beginning around 10am and 2pm each day* and recording information about seating type, location, and activity. The study was planned by Jeremy Buhler, Julie Mitchell, and Trish Rosseel. Please contact Jeremy Buhler at jeremy.buhler@ubc.ca if you have questions.
DOI: 10.5683/sp2/dlkgzv
title: UBC Library Circulation of Physical Items

description: Circulation transaction records for all items with barcodes checked out during the report date range. Excludes use of ebooks and ejournals. Please contact Jeremy Buhler at jeremy.buhler@ubc.ca if you have questions.
DOI: 10.5683/sp2/w2yhnh
title: UBC Library LibQUAL Survey Results: User Perceptions of Library Service

description: LibQUAL is a standardised survey instrument developed by the Association of Research Libraries (ARL) that measures user perceptions of library services. Libraries implement LibQUAL periodically to better understand user priorities and to monitor library performance relative to student and faculty expectations. The survey questions focus on three service areas: library collections and access customer services library physical spaces UBC Library has released LibQUAL data from 2007, 2010, and 2013. Please contact Jeremy Buhler at jeremy.buhler@ubc.ca if you have questions.
DOI: 10.5683/sp2/bh5kph
title: UBC Library Catalogue of Physical Materials

description: UBC Library catalogue of physical materials. Snapshot extracted from Voyager on the specified day. Excludes use of ebooks and ejournals. Please contact Jeremy Buhler at jeremy.buhler@ubc.ca if you have questions.