GSE80496

Diagnosis of childhood bacterial and viral infection using host RNA expression - Meningococcal validation cohort

Whole-study status Exploratory only

Dataset can inform exploration but is not strong enough for primary analysis.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source
GEO
Assay
microarray
Organism
Homo sapiens
Whole-study samples
45 samples
Specimen
Biofluid
Reported/interpreted study design
Patient biofluid vs healthy control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Levin M
Contact name
Michael Levin
Submission date
2016-04-20
Last update
2017-03-20
Organization
Imperial College London
Department
Paediatrics
Public date
2016-08-29
Experiment types
Expression profiling by array
Platforms
GPL6883 Illumina HumanRef-8 v3.0 expression beadchip
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA319053

Summary

Genome-wide analysis of transcriptional profiles in children <17 years of age with bacterial or viral infections or with clinical features suggestive of infection.

Overall design

Patients were recruited at or after presentation to hospital. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human Ref8 Beadchips. Numbers of arrays analysed were as follows: Meningococal disease (n=24), Healthy adult controls (n=21)

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
45 GSM samples
 Primary source
recount3

Planned trusted source for processed count availability.

 No match found
Expression Atlas

Planned source for curated expression experiment links.

 No match found
PubMed

Primary GEO citations and related PubMed articles that mention this dataset.

3 linked publications 3 DOIs

Primary publication

  1. Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. JAMA, 2016

Related publications

  1. Lactate-Associated Gene Signatures as Predictors: A Comprehensive Analysis of Immune Profiles in Sepsis. Journal of intensive care medicine, 2026
  2. Key Common Genes with LTF and MMP9 Between Sepsis and Relapsed B-Cell Lineage Acute Lymphoblastic Leukemia in Children. Biomedicines, 2025
Available

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Ready after review
97% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

  • Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Assay context may require expert handling before DESeq2-style analysis.

Why This Is Ranked Here

Tumor vs normal
Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

  • Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
  • Disease context Sepsis Disease context came from Normalization rules.
  • Likely case group Sepsis or systemic inflammatory response 24 samples
  • Likely control group Healthy control 21 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
  • Interpreted disease metadata: Infectious disease or host response, Sepsis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 3 publications; 3 DOIs available: PMID 27552617, PMID 41007866, PMID 42286943.
  • Publication context: Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children.. JAMA, 2016. PMID 27552617. DOI 10.1001/jama.2016.11236.
  • Publication context: Key Common Genes with LTF and MMP9 Between Sepsis and Relapsed B-Cell Lineage Acute Lymphoblastic Leukemia in Children.. Biomedicines, 2025. PMID 41007866. DOI 10.3390/biomedicines13092307.
  • Publication context: Lactate-Associated Gene Signatures as Predictors: A Comprehensive Analysis of Immune Profiles in Sepsis.. Journal of intensive care medicine, 2026. PMID 42286943. DOI 10.1177/08850666261458765.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

225 fields

Sample Group Preview

45 rows shown Show Hide
Study totals: Case 24 | Control 21 | Unassigned 0 | Excluded 0 | Ambiguous 0 45 rows shown
Group Role Accession Title Source / characteristics Reason
Sepsis or systemic inflammatory response Case GSM2128390 Meningitis Sepsis 01 Whole Blood from patient with Sepsis and Meningitis Gender: Female; Disease state: Sepsis and meningitis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128391 Meningitis Sepsis 02 Whole Blood from patient with Sepsis and Meningitis Gender: Female; Disease state: Sepsis and meningitis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128392 Meningitis Sepsis 03 Whole Blood from patient with Sepsis and Meningitis Gender: Female; Disease state: Sepsis and meningitis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128393 Sepsis 01 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128394 Sepsis 02 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128395 Sepsis 03 Whole Blood from patient with Sepsis Gender: Female; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128396 Sepsis 04 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128397 Sepsis 05 Whole Blood from patient with Sepsis Gender: Female; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128398 Sepsis 06 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128399 Sepsis 07 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128400 Sepsis 08 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128401 Sepsis 09 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128402 Sepsis 10 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128403 Sepsis 11 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128404 Sepsis 12 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128405 Sepsis 13 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128406 Sepsis 14 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128407 Sepsis 15 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128408 Sepsis 16 Whole Blood from patient with Sepsis Gender: Female; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128409 Sepsis 17 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128410 Sepsis 18 Whole Blood from patient with Sepsis Gender: Female; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128411 Sepsis 19 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128412 Sepsis 20 Whole Blood from patient with Sepsis Gender: Female; Disease state: Sepsis Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM2128413 Sepsis 21 Whole Blood from patient with Sepsis Gender: Male; Disease state: Sepsis Explicit sample label case marker detected.
Healthy control Control GSM2128369 Healthy Control 01 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128370 Healthy Control 02 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128371 Healthy Control 03 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128372 Healthy Control 04 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128373 Healthy Control 05 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128374 Healthy Control 06 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128375 Healthy Control 07 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128376 Healthy Control 08 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128377 Healthy Control 09 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128378 Healthy Control 10 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128379 Healthy Control 11 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128380 Healthy Control 12 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128381 Healthy Control 13 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128382 Healthy Control 14 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128383 Healthy Control 15 Whole Blood from healthy control Gender: Female; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128384 Healthy Control 16 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128385 Healthy Control 17 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128386 Healthy Control 18 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128387 Healthy Control 19 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128388 Healthy Control 20 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.
Healthy control Control GSM2128389 Healthy Control 21 Whole Blood from healthy control Gender: Male; Disease state: Healthy Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.