Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 20

System / cell line: identified ✕ Assay: ontology ✕ Clear

System-based proteomic analysis of the interferon response in human liver cells.

PMID 15287976 · PMC507879 · Genome biology · 2004 · 7 claims · 4 setups

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ICAT-based quantitative proteomics identified 1,364 proteins in Huh7 cells at <5% false-positive rate, with 54 induced and 24 repressed >2-fold by IFN treatment

huh7 computational icat gene interaction
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins.

PMID 16948836 · PMC1794545 · Genome biology · 2006 · 8 claims · 6 setups

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Identified 1543 proteins in urine from ten healthy donors while essentially eliminating false-positive identifications

urine pooled urinary identified sds-page albumin decoy
SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.

PMID 39300285 · PMC11413210 · Communications biology · 2024 · 8 claims · 8 setups

Has reproduction · 78

A shared wound healing gene set (P2-WHGs, 146 genes) is constitutively expressed in uninjured oral mucosa but not in uninjured skin

injured normal p2-whgs oral bulk single-cell gene
Identifying synonymous regulatory elements in vertebrate genomes.

PMID 15980499 · PMC1160227 · Nucleic acids research · 2005 · 7 claims · 4 setups

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SynoR is a tool that performs de novo genome-wide identification of synonymous regulatory elements (SREs) using evolutionarily conserved TFBS modules as seeds

genome genes genome-wide gene tissue-specificity
Large-scale and high-confidence proteomic analysis of human seminal plasma.

PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

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923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

seminal same list combined sds-page database decoy
Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups

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Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome

pooled albumin-bound analysis mudpit immunoaffinity bca
Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups

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CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.

spleen cd45 hox11+ lc-ms rt-pcr immunofluorescence
A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups

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iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ

pooled plasma prefractionated immunodepleted itraq 1-dimensional fluorescence-based
In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

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This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

vastus skeletal spectra identified phosphopeptide in-solution strong
Proteomic-based identification of maternal proteins in mature mouse oocytes.

PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

mature mii identified tissues sds-page acid gene
Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors.

PMID 16901338 · PMC1779605 · Genome biology · 2006 · 8 claims · 4 setups

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491 proteins were identified in human tear fluid using in-gel digestion and LC-MS/MS/MS3 on LTQ-FT and LTQ-Orbitrap instruments

closed-eye tear analysis sds-page in-solution gene
Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

PMID 17888167 · PMC2082044 · BMC genomics · 2007 · 8 claims · 6 setups

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A proposed coupled two-way clustering (CTWC/SPC) method combined with a GO-based functional concept consistency score can identify compact, robust gene subsets that define clinically meaningful DLBCL subtypes

dlbcl identified microarray oligonucleotide coupled
Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

paired list differentially oscc 2-de gene interaction
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

gingivalis whole-cell comparative gene
Sys-BodyFluid: a systematical database for human body fluid proteome research.

PMID 18978022 · PMC2686600 · Nucleic acids research · 2009 · 6 claims · 4 setups

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Sys-BodyFluid is a web-based database integrating proteomic data from 11 human body fluids (plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, milk, amniotic fluid), containing over 10,000 proteins

body curated proteins literature sequence cross-body-fluid
Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

PMID 18672925 · PMC2680441 · Journal of proteome research · 2008 · 8 claims · 6 setups

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34 immunoreactive protein spots were detected in 2DE Western blots probed with HCC patient sera but not normal sera

hepg2 excised identified recombinant two-dimensional western in-gel
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

Has reproduction · 66

A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons

fmr1-adarcd-v5 single bioinformatic drosophila immunofluorescence western bulk
Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 87

Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

breast lung colorectal melanoma single-cell gene reactome
Human spermatozoa contain multiple targets for protein S-nitrosylation: an alternative mechanism of the modulation of sperm function by nitric oxide?

PMID 17683036 · PMC2777308 · Proteomics · 2007 · 7 claims · 5 setups

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Human sperm proteins undergo S-nitrosylation upon exposure to NO donors, detectable by the biotin switch assay

percoll-washed fixed pooled excised biotin situ streptavidin-agarose
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.

PMID 38860884 · PMC11261899 · Microbial genomics · 2024 · 7 claims · 3 setups

Has reproduction · 75

PHA4GE developed a set of standardized contextual data tags (five fields plus controlled-vocabulary terms) for annotating pathogen sequence datasets with known quality issues.

fda pha4ge genomic metagenomic community ontology

Experiments

System-based proteomic analysis of the interferon response in human liver cells.

The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins.

SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.

Identifying synonymous regulatory elements in vertebrate genomes.

Large-scale and high-confidence proteomic analysis of human seminal plasma.

Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

Proteomic-based identification of maternal proteins in mature mouse oocytes.

Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors.

Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

Sys-BodyFluid: a systematical database for human body fluid proteome research.

Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

Human spermatozoa contain multiple targets for protein S-nitrosylation: an alternative mechanism of the modulation of sperm function by nitric oxide?

PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.