How to Use the Candida Genome Database.

Marek S Skrzypek, Jonathan Binkley, Gavin Sherlock

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it

0cells of the map it votes in

3citing papers in PubMed

–field-weighted citation impact

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

3 citing papers in PubMed.

Transcriptome Analysis of Human Dermal Cells Infected with Candida auris Identified Unique Pathogenesis/Defensive Mechanisms Particularly Ferroptosis.Mycopathologia · 2024
Article
Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling.BMC genomics · 2017
Article
Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens.Frontiers in microbiology · 2016
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

3 authors.

Marek S SkrzypekDepartment of Genetics, Stanford University Medical School, S225 Grant Building, 259 Campus Drive, Stanford, CA, 94305-5120, USA.

Jonathan BinkleyDepartment of Genetics, Stanford University Medical School, S225 Grant Building, 259 Campus Drive, Stanford, CA, 94305-5120, USA.

Gavin SherlockDepartment of Genetics, Stanford University Medical School, S225 Grant Building, 259 Campus Drive, Stanford, CA, 94305-5120, USA. gsherlock@stanford.edu.

Funding

Genomic Database for Candida AlbicansR01DE015873 · NIDCR · STANFORD UNIVERSITY · PI Gavin J Sherlock · 2004 to 2026

$11.7M

NIDCR NIH HHS R01 DE015873

6 · The paper itself

Abstract

Studying Candida biology requires access to genomic sequence data in conjunction with experimental information that provides functional context to genes and proteins. The Candida Genome Database (CGD) integrates functional information about Candida genes and their products with a set of analysis tools that facilitate searching for sets of genes and exploring their biological roles. This chapter describes how the various types of information available at CGD can be searched, retrieved, and analyzed. Starting with the guided tour of the CGD Home page and Locus Summary page, this unit shows how to navigate the various assemblies of the C. albicans genome, how to use Gene Ontology tools to make sense of large-scale data, and how to access the microarray data archived at CGD.

Indexed as

Databases, GeneticGenome, FungalCandidaCandida albicansComputational BiologyGene OntologyGenetic LociGenomicsCandidaExpression analysisGene ontologyGenome databaseGO slim

Identifiers

PMID26519061

DOI10.1007/978-1-4939-3052-4_1

PMCPMC4896156

What OpenQuestion holds

Textmetadata

LicenceTDM

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.