Construction of <i>Escherichia coli</i> K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Construction of <i>Escherichia coli</i> K‐12 in‐frame, single‐gene knockout mutants: the Keio collection is a dataset published in Molecular Systems Biology (2006). On theSindex it has a DataRank of 19.2, placing it in the top 6.3% of the data-sharing corpus. It has been cited 8,210 times, with 194 citing works in its 1-hop citation network. Its calibrated FAIR score is 41/100.
Abstract
We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).
›Data sources & pipeline
FAIR Checklist
Context only (not used in score)- Has DOI
- Open Access
- Dataset classification
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
DataRank Breakdown
Base Score Contribution
1.3
From this paper's citation signal
Citation Network Contribution
17.8
From 194 citing papers with measurable signal
Top 5 citers driving the network score
Ranked by citation count — the same ordering the engine uses when summing log1p(Cq) over citers.
- One-step inactivation of chromosomal genes in <i>Escherichia coli</i> K-12 using PCR productsProceedings of the National Academy of Sciences200015,089 citationsDataRank 1.4
- Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with AcetylationCell Reports2013769 citationsDataRank 12.7
- Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotationGenome Research2007192 citationsDataRank 6.8
- Low mutational load and high mutation rate variation in gut commensal bacteriaPLOS Biology202083 citationsDataRank 2.0
- Coenzyme biosynthesis in response to precursor availability reveals incorporation of β-alanine from pantothenate in prototrophic bacteriaJournal of Biological Chemistry202310 citationsDataRank 0.489
Why this DataRank?
DataRank blends this paper's own citation count with the influence of the papers that cite it. Here, roughly 7% comes from its base citations and 93% from the citation network (194 citing papers contributed measurable signal).
- Base score B(p)
- log1p(citation_count) — grows sub-linearly, so a paper with 1,000 citations is not 10× a paper with 100.
- Network N(p)
- Σ over citers of log1p(Cq) ÷ max(outdegreeq, 1). Being cited by a highly-cited paper with few references counts most.
- Damping factor d = 0.85
- DataRank = (1−d)·B(p) + d·N(p) — the two cards above are each already multiplied by their share.
- Self-citations excluded
- Citers sharing any OpenAlex author ID with this paper are filtered out before the network sum.
Citers are pulled from OpenAlex sorted by cited_by_count:descand capped per paper, so when the cap binds we keep the highest-signal references and the score is reproducible across reruns.
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