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).

• Alterations in candidate genes PHF2, FANCC, PTCH1 and XPA at chromosomal 9q22.3 region: pathological significance in early- and late-onset breast carcinoma.

  PMID 18990233 · PMC2633285 · Molecular cancer · 2008 · 8 claims · 5 setups

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  PHF2, FANCC and PTCH1 show high frequency of alterations (deletion/methylation) compared to XPA in both early- and late-onset breast carcinoma groups

  invasive breast normal microsatellite methylation sscp

• Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

  PMID 10408842 · PMC2362327 · British journal of cancer · 1999 · 8 claims · 3 setups

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  No mutations were found in the coding region of GDNF in any of the 36 brain tumours analysed

  sporadic tumour tumour-derived pcr loss semi-quantitative

• Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

  PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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  Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

  genomic maternal 22qtdr chromosome semi-quantitative pcr fish

• Intragenic homozygous deletions of MTS1 gene in gastric cancer in Taiwan.

  PMID 8957063 · PMC5921000 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 4 setups

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  Homozygous deletions of exon 1 of the MTS1 gene were found in 5 of 55 (9.1%) primary gastric tumors.

  gastric pcr tumor southern pcr direct

• Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

  PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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  Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

  matched bone leukemia diagnosis snp flow quantitative

• Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

  PMID 15785740 · PMC2361973 · British journal of cancer · 2005 · 8 claims · 2 setups

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  D-loop mutation frequency is significantly higher in both noncancerous and tumour liver tissue of HCC/HBV patients than in normal control liver

  liver pcr

• Sequence context affects the rate of short insertions and deletions in flies and primates.

  PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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  The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

  chimpanzee simulans chimp primate comparative direct nucleotide

• Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

  PMID 18281252 · PMC2443276 · Carcinogenesis · 2008 · 7 claims · 4 setups

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  Cigarette smoking is associated with a higher frequency of somatic mtDNA mutations in buccal cells

  buccal subject ttge real-time pcr-based

• p53 mutations in urinary bladder cancer.

  PMID 11384101 · PMC2363660 · British journal of cancer · 2001 · 6 claims · 5 setups

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  p53 mutations are strongly associated with high-grade/high-stage bladder tumors and are nearly absent in lowly malignant tumors (Ta, G1-G2a)

  urinary tumor patients single multiplex-pcr dyedeoxy loss

• A review on the molecular diagnostics of Lynch syndrome: a central role for the pathology laboratory.

  PMID 19929944 · PMC3837620 · Journal of cellular and molecular medicine · 2010 · 8 claims · 7 setups

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  Lynch syndrome is caused by germline mutations in the mismatch repair genes MLH1, MSH2, MSH6 or PMS2

  colorectal tumour sporadic germline msi immunohistochemistry mlh1

• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

  PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

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  BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

  reads yoruban cytogenetically predicted simulated paired-end whole-genome

• Ovarian cancer has frequent loss of heterozygosity at chromosome 12p12.3-13.1 (region of TEL and Kip1 loci) and chromosome 12q23-ter: evidence for two new tumour-suppressor genes.

  PMID 9155043 · PMC2228239 · British journal of cancer · 1997 · 8 claims · 4 setups

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  Two commonly deleted regions on chromosome 12 were identified in ovarian cancer: 12p12.3-13.1 (6/23 samples) and 12q23-ter (7/23 samples)

  ovarian loh pcr-sscp multiplex

• Molecular tumor profiling: translating genomic insights into clinical advances.

  PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

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  Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

  breast ovarian panel tumor gene-expression candidate-gene large-scale

• L2L: a simple tool for discovering the hidden significance in microarray expression data.

  PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

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  L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

  mammalian user-supplied diabetic uniprot compiled l2l re-analysis

• A novel Twinkle (PEO1) gene mutation in a Chinese family with adPEO.

  PMID 18989381 · PMC2579934 · Molecular vision · 2008 · 8 claims · 5 setups

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  Two-point linkage analysis maps this Chinese adPEO family to the PEO1 (Twinkle) locus on chromosome 10q23.3-24.3, with the other three candidate genes excluded.

  members family biceps proband two-point direct muscle

• Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.

  PMID 11985787 · PMC5927018 · Japanese journal of cancer research : Gann · 2002 · 6 claims · 3 setups

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  MN mutations occur significantly more frequently in sporadic colorectal cancer (56%) than in gastric cancer (25%)

  sporadic same multilocus pcr-simple

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative

• Current status and the future for the genetics of type I diabetes.

  PMID 19956094 · PMC2805458 · Genes and immunity · 2009 · 8 claims · 7 setups

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  A T1DGC genome-wide association meta-analysis of >7500 cases and >9000 controls identified 42 distinct genomic locations associated with T1D at P<10^-6.

  asp subjects t1dgc cases genome-wide mhc candidate