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 39

System / cell line: tumor ✕ Assay: mass ✕ Clear

An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention.

PMID 16351756 · PMC1866378 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Meta-analysis of two independent BALB-neuT transcription profiling studies can identify new TAA candidates usable instead of or with Her2

balb-neut normal breast probe microarray statistical enrichment
Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

PMID 19920251 · PMC2812789 · Science signaling · 2009 · 7 claims · 8 setups

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Oncogenic FGFR1 directly phosphorylates PKM2 at tyrosine 105 (Y105), inhibiting its enzymatic activity

293t kg-1a recombinant h1299 ms-based co-transfection enzymatic
Two cases of isolated diffuse mesangial sclerosis with WT1 mutations.

PMID 16479084 · PMC2733967 · Journal of Korean medical science · 2006 · 8 claims · 7 setups

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Two female infants with isolated diffuse mesangial sclerosis (IDMS) and early-onset end-stage renal failure carried heterozygous WT1 mutations (exon 8 366Arg>His; exon 9 396Asp>Tyr)

genomic kidney blood kidneys direct parental renal
Pathway analysis of kidney cancer using proteomics and metabolic profiling.

PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

ccrcc rcc computational random gel immunoblotting immunohistochemistry
Profiling critical cancer gene mutations in clinical tumor samples.

PMID 19924296 · PMC2774511 · PloS one · 2009 · 7 claims · 4 setups

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OncoMap, a panel of ~400 mass-spectrometric genotyping assays targeting 33 cancer genes, enables robust mutation profiling of clinical fresh-frozen and FFPE tumor DNA.

clinical fresh same pediatric mass sanger barcoded
Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups

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ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

paired icat-labeled spectra naf icat sds-page liquid
Proteomics as a tool for biomarker discovery.

PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

serum laser ovarian seldi-tof two-dimensional gene
Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

lung scanned excised peptide 2-d 2-de maldi-tof-ms
Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

fresh-frozen same banked resected array mutational pcr
Proteomics: characterizing the cogs in the machinery of life.

PMID 14630521 · PMC1241753 · Environmental health perspectives · 2003 · 8 claims · 5 setups

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Protein expression patterns in blood serum, detected via SELDI-TOF mass spectrometry and analyzed with a genetic algorithm, can distinguish ovarian cancer patients from healthy individuals with very high sensitivity and specificity.

blood lung hemoglobin proteins seldi-tof proteome tandem
Defining disease with laser precision: laser capture microdissection in gastroenterology.

PMID 18619446 · PMC3736118 · Gastroenterology · 2008 · 8 claims · 8 setups

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LCM allows isolation of pure cell populations from heterogeneous tissue without damaging DNA, RNA, or protein integrity.

esophagus gastric colorectal colonic maldi cdna profiling
Microproteomics: analysis of protein diversity in small samples.

PMID 18271009 · PMC2743962 · Mass spectrometry reviews · 2008 · 8 claims · 8 setups

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Changes in gene/mRNA expression often do not correlate well with changes in protein expression, due to precursor cleavage, post-translational modification, localization, and variable protein lifetimes.

lcm-dissected single few dense gel maldi capillary
Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups

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Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas

resected thymic previously mass dideoxynucleotide array
A pilot study of proteomic profiles of human hepatocellular carcinoma in the United States.

PMID 19535095 · PMC2859432 · The Journal of surgical research · 2009 · 8 claims · 3 setups

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19 protein spots showed significant (>2-fold, P<0.01) abundance differences between HCC tumor and nonmalignant liver tissue

liver tryptic solubilized gel maldi-tof quantification
Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

hla-b44 plasma macrophages complement proteomics shotgun cap
The use of laser capture microscopy in proteomics research--a review.

PMID 15502248 · PMC3839334 · Disease markers · 2004 · 8 claims · 8 setups

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LCM allows purification of specific, histologically defined cell populations from heterogeneous tissue for downstream proteomic analysis

breast prostate esophageal head maldi-tof automated two-dimensional
Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

PMID 15502247 · PMC3839398 · Disease markers · 2004 · 8 claims · 8 setups

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Proteomics approaches (2D Western blot, protein microarray, multiplex ELISA) can identify tumor antigen-directed autoantibodies as candidate cancer biomarkers

lung pancreatic hepatocellular renal gel microarray multiplex
Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

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An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

mg-thymoma colon exon fluorescent reverse
Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups

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wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables

serum colon glioblastoma synthetic seldi-tof gene computational
Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

PMID 18416831 · PMC2377273 · BMC cancer · 2008 · 6 claims · 4 setups

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Three protein spots were significantly altered in abundance between metastase-positive and metastase-negative breast cancer patient groups

excised formalin-fixed log-normalized two-dimensional liquid immunohistochemistry

Experiments

An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention.

Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

Two cases of isolated diffuse mesangial sclerosis with WT1 mutations.

Pathway analysis of kidney cancer using proteomics and metabolic profiling.

Profiling critical cancer gene mutations in clinical tumor samples.

Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

Proteomics as a tool for biomarker discovery.

Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

Proteomics: characterizing the cogs in the machinery of life.

Defining disease with laser precision: laser capture microdissection in gastroenterology.

Microproteomics: analysis of protein diversity in small samples.

Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

A pilot study of proteomic profiles of human hepatocellular carcinoma in the United States.

Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

The use of laser capture microscopy in proteomics research--a review.

Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.