Evidence map›Paper›PMID 37496087›Full record

Observational studyGenome biology2023

ISLET: individual-specific reference panel recovery improves cell-type-specific inference.

Hao Feng, Guanqun Meng, Tong Lin, Hemang Parikh, Yue Pan, Ziyi Li, Jeffrey Krischer, Qian Li

Abstract readObservational Study
PubMed Full text at PMC Publisher
In one paragraph

Observational study in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Virtual tissue expression analysis.Bioinformatics (Oxford, England) · 2024
    Article
  3. Article
  4. Article
  5. Article
  6. bioRxiv : the preprint server for biology · 2023
    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

8 authors.

Hao FengDepartment of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA. hxf155@case.edu.
Guanqun MengDepartment of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
Tong LinDepartment of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
Hemang ParikhHealth Informatics Institute, University of South Florida, Tampa, FL, 33620, USA.
Yue PanDepartment of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
Ziyi LiDepartment of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
Jeffrey KrischerHealth Informatics Institute, University of South Florida, Tampa, FL, 33620, USA.
Qian LiDepartment of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. qian.li@stjude.org.ORCID 0000-0001-9874-3555

Funding

NIDDK Network Coordinating UnitU24DK097771 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Shuibing Chen, Jeffrey S. Grethe · 2013 to 2026
$20.9M
Statistical models for intratumor heterogeneity of tumor-infiltrated leukocytes in lung cancerR03CA270725 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI LI, ZIYI · 2022 to 2023
$162k
NCI NIH HHS R03 CA270725NIDDK NIH HHS U24 DK097771
6 · The paper itself

Abstract

We propose a statistical framework ISLET to infer individual-specific and cell-type-specific transcriptome reference panels. ISLET models the repeatedly measured bulk gene expression data, to optimize the usage of shared information within each subject. ISLET is the first available method to achieve individual-specific reference estimation in repeated samples. Using simulation studies, we show outstanding performance of ISLET in the reference estimation and downstream cell-type-specific differentially expressed genes testing. We apply ISLET to longitudinal transcriptomes profiled from blood samples in a large observational study of young children and confirm the cell-type-specific gene signatures for pancreatic islet autoantibody. ISLET is available at https://bioconductor.org/packages/ISLET .

Indexed as

Islets of LangerhansAutoantibodiesChildChild, PreschoolComputer SimulationGene Expression ProfilingHumansTranscriptomeAutoantibodiesCell-type-specific differential expressionDeconvolutionIndividual-specific reference panelTemporal measures

Identifiers

PMID37496087
PMCPMC10373385

What OpenQuestion holds

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LicenceCC BY
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.