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 23

System / cell line: across ✕ Assay: proteomic ✕ Clear

Identification of biomarkers from mass spectrometry data using a "common" peak approach.

PMID 16869977 · PMC1550264 · BMC bioinformatics · 2006 · 8 claims · 1 setups

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"Common" peaks—those exhibited by many subjects—can be identified and used as biomarkers in high-dimensional mass spectrometry data

serum mass
Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

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Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

plasma ppp reference identification quantitative specimen
Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

serum frozen ig-depleted clinical seldi-tof maldi lc-ms
Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

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SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

serum seldi dlbcl pooled seldi-tof-ms proteinchip decision
INTERFEROME: the database of interferon regulated genes.

PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

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INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

chimp ifn-treated tissues irg microarray in-house basal
Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

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LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

surgically tryptic set lysates lc-ms mascot immunohistochemistry
Limitations in SELDI-TOF MS whole serum proteomic profiling with IMAC surface to specifically detect colorectal cancer.

PMID 19689818 · PMC2743709 · BMC cancer · 2009 · 7 claims · 3 setups

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The previously reported classifier (m/z 8,132 and 4,002) failed to discriminate CRC patients from healthy volunteers in this independent validation cohort

serum pooled seldi-tof comparative decision
Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

breast sars serum tumour microarray custom mass
Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups

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QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies

serum pooled duplicate full seldi-tof principal technical
Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.

PMID 18984079 · PMC2679897 · American journal of obstetrics and gynecology · 2008 · 8 claims · 7 setups

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Women with severe preeclampsia present a unique urinary proteomic fingerprint distinguishable from controls.

urine placenta placental seldi-tof tandem spiking
Proteomic profiling in ovarian cancer.

PMID 19955909 · PMC7319026 · International journal of gynecological cancer : official journal of the International Gynecological Cancer Society · 2009 · 8 claims · 6 setups

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No validated or cost-efficient screening program exists for ovarian cancer; physical exam, CA125, and transvaginal ultrasound lack sufficient sensitivity/specificity for early-stage detection.

serum tumor rolling mass microarray
Fingerprinting cancer development.

PMID 14694892 · PMC1241638 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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Protein microarrays can detect phosphoprotein fingerprints that identify early-stage cancer or monitor drug toxicity.

prostate blood model genes microarray proteomic gene
miRGator: an integrated system for functional annotation of microRNAs.

PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

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miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

genome predicted tissues organs computational functional mirna
Toxicogenomics: an emerging discipline.

PMID 12460812 · PMC1241126 · Environmental health perspectives · 2002 · 8 claims · 6 setups

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Toxicogenomics applies genomic tools (microarrays, proteomics, metabolomics) to characterize how cells and organisms respond to chemical/drug exposures.

drug stated acetaminophen tissues microarray gene genomic
Prospective health care: the second transformation of medicine.

PMID 16522218 · PMC1431721 · Genome biology · 2006 · 8 claims · 7 setups

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Predictive biomarkers (genomic, proteomic, metabolomic) will enable quantification of disease risk and anticipation of onset before pathological damage occurs.

cancer circulating breast population gene-expression proteomic 21-gene
RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.

PMID 19789336 · PMC2927135 · Cancer research · 2009 · 8 claims · 8 setups

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K-RAS and N-RAS mutation status differentially determine the level of TNFα-induced apoptosis in an isogenic colon carcinoma cell panel

isogenic same conditioned dld-1 flow luminex immunoblot
Microbial metagenomics.

PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

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Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

gastrointestinal acid ocean group metagenomic shotgun comparative
Application of proteomics in the study of tumor metastasis.

PMID 15862116 · PMC5172469 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 8 setups

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Cell function is directly regulated through proteins, not genes or mRNA, so metastasis-related gene findings need protein-level validation via proteomics.

young metastatic hepatocellular lines microarray 2de cdna
Microarray analysis: genome-scale hypothesis scanning.

PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

drosophila yeast diffuse breast microarray integrated gene
HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups

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HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

t-cell identified gel maldi-tof bioinformatics

Experiments

Identification of biomarkers from mass spectrometry data using a "common" peak approach.

Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

INTERFEROME: the database of interferon regulated genes.

Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

Limitations in SELDI-TOF MS whole serum proteomic profiling with IMAC surface to specifically detect colorectal cancer.

Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.

Proteomic profiling in ovarian cancer.

Fingerprinting cancer development.

miRGator: an integrated system for functional annotation of microRNAs.

Toxicogenomics: an emerging discipline.

Prospective health care: the second transformation of medicine.

RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects.

Microbial metagenomics.

Application of proteomics in the study of tumor metastasis.

Microarray analysis: genome-scale hypothesis scanning.

HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.