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 16

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

Characterisation and protein expression profiling of annexins in colorectal cancer.

PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

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Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

dukes colorectal immunised whole-cell gel immunohistochemistry elisa
Liver fatty acid binding protein expression in colorectal neoplasia.

PMID 15138477 · PMC2409459 · British journal of cancer · 2004 · 8 claims · 5 setups

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L-FABP is consistently lost/decreased in colorectal cancer compared with paired normal colon tissue

paired excised formalin-fixed normal gel maldi-tof immunohistochemistry
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

genes hela proteins worm co-expression quantitative functional
Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

PMID 19856998 · PMC2924679 · Journal of proteome research · 2009 · 7 claims · 4 setups

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RCL2/CS100-fixed tissues yield peptide and protein identifications by nanoRPLC-MS/MS comparable to matched fresh-frozen tissues, with proteome coverage not obviously compromised by fixation.

colonic rcl2 colon nanorplc-ms extraction laser
Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

PMID 19789534 · PMC2768081 · British journal of cancer · 2009 · 8 claims · 7 setups

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Cathepsin D, identified via comparative 2D PAGE of conditioned media from RCC cell lines vs normal renal cultures, is a candidate secreted biomarker of RCC

htb49 excised conditioned urine page maldi western
Addressing the obesity epidemic: a genomics perspective.

PMID 17362622 · PMC1893129 · Preventing chronic disease · 2007 · 8 claims · 8 setups

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Obesity is a multifactorial disorder reflecting complex interactions of genes, environment, and lifestyle

identical fraternal children younger twin family longitudinal
A proteomic analysis of IVF follicular fluid in women

PMID 18980758 · PMC3916005 · Fertility and sterility · 2009 · 8 claims · 4 setups

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2D-PAGE proteomic evaluation of follicular fluid can identify potential biomarkers distinguishing good versus poor IVF responders in matched patient pairs

follicular excised clinical polyacrylamide liquid direct
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
The many uses of a genome sequence.

PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

recombinant mammalian chromosome chimpanzee x-ray quantitative tiling
Back to basics.

PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

chromosome pendrin yeast carbonic genome gene mudpit
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

saccharomyces homo bank computational yeast tandem
Considerations regarding the genetics of obesity.

PMID 19037210 · PMC2682366 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 8 setups

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Genetic factors account for 40-70% of the variance in human adiposity

monozygotic subjects european children twin genome-wide association
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.

PMID 18179696 · PMC2231339 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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AGML 2.0 is a comprehensive XML representation for 2-DE experiments comprising identification, protocol (MI2DG), and gel sections

general gel excised clinical 2-dimensional differential mass
Interactome networks: the state of the science.

PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

genes tnfα orf proteins yeast tandem interference
Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

matched excised additional formalin-fixed 2-d lc-ms quantitative
Whither genomics?

PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

mammalian budding yeast general expression genome-wide synthetic

Experiments

Characterisation and protein expression profiling of annexins in colorectal cancer.

Liver fatty acid binding protein expression in colorectal neoplasia.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

Addressing the obesity epidemic: a genomics perspective.

A proteomic analysis of IVF follicular fluid in women

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

The many uses of a genome sequence.

Back to basics.

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

Considerations regarding the genetics of obesity.

An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.

Interactome networks: the state of the science.

Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

Whither genomics?