Categorization of 33 computational methods to detect spatially variable genes from spatially resolved transcriptomics data.

Guanao Yan, Shuo Harper Hua, Jingyi Jessica Li

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In one paragraph

Article in ArXiv, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

Updated by
Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data.2025

5 · Who and what money

Authors and funding

3 authors.

Guanao YanDepartment of Statistics, University of California, Los Angeles, CA 90095-1554.

Shuo Harper HuaDepartment of Biomedical Data Science, Stanford University, Stanford, CA 94305.

Jingyi Jessica LiDepartment of Statistics, University of California, Los Angeles, CA 90095-1554.

Funding

Statistical Methods for Elucidating Regulatory Mechanisms and Functional Impacts of Transcriptome Variation at Population and Single-Cell ScalesR35GM140888 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, JINGYI JESSICA · 2021 to 2025

$2.0M

Robust Identification and accurate quantification of RNA transcripts on a system wide scaleR01GM120507 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, JINGYI JESSICA · 2016 to 2021

$1.7M

NIGMS NIH HHS R01 GM120507NIGMS NIH HHS R35 GM140888

6 · The paper itself

Abstract

In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 33 state-of-the-art methods, categorizing SVGs into three types: overall, cell-type-specific, and spatial-domain-marker SVGs. Our review explains the intuitions underlying these methods, summarizes their applications, and categorizes the hypothesis tests they use in the trade-off between generality and specificity for SVG detection. We discuss challenges in SVG detection and propose future directions for improvement. Our review offers insights for method developers and users, advocating for category-specific benchmarking.

Identifiers

PMID38855546

PMCPMC11160866

What OpenQuestion holds

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LicenceCC BY-NC-ND

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Registered trials

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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.