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 51

System / cell line: colon ✕ Assay: cancer ✕ Clear

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

colon gbm cancer dbtrg array pcr colony
Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 8 claims · 8 setups

Has reproduction · 48

A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates

tcga-coad ncbi-geo tisidb gepia rna-seq tumor-infiltrating gene
Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

PMID 15138480 · PMC2410281 · British journal of cancer · 2004 · 7 claims · 5 setups

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MBD3 is not a major target of genetic or epigenetic alteration in colon and lung cancer

colon normal pcr-sscp rt-pcr northern
MMASS: an optimized array-based method for assessing CpG island methylation.

PMID 17041235 · PMC1635254 · Nucleic acids research · 2006 · 8 claims · 7 setups

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MMASS-v2 (optimized AciI/HinP1I/HpyCH4IV/HpaII enzyme combination with McrBC digestion) offers improved sensitivity and statistical power for microarray-based CpG island methylation detection compared to MMASS-v1, MMASS-sub and the Nouzova method

hct116 sssi-methylated hcgi12k methylation spike-in cobra
Raf-1 activation disrupts its binding to keratins during cell stress.

PMID 15314064 · PMC2172217 · The Journal of cell biology · 2004 · 8 claims · 8 setups

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Raf-1 kinase associates directly with keratin K8 (not K18), independent of Raf kinase activity and independent of Ras-Raf interaction

ht29 transgenic bhk-21 bhk co-immunoprecipitation co-transfection oxidative
Genomic and epigenetic instability in colorectal cancer pathogenesis.

PMID 18773902 · PMC2866182 · Gastroenterology · 2008 · 8 claims · 7 setups

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Genomic instability (CIN or MSI) is a key early molecular step in colorectal tumorigenesis that may initiate rather than merely accompany the adenoma-carcinoma sequence

colon embryonic colorectal inter immunohistochemistry karyotype
H-DBAS: human-transcriptome database for alternative splicing: update 2010.

PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

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RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

dld-1 rna-seq western real-time
Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

paired colorectal genome normal quma auma bioinformatic
Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 8 claims · 8 setups

Has reproduction · 68

The integrated stress response (ISR) induces CRC cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

ht29-derived ht29 nod rna-seq faire-qpcr chip-seq
Low frequency of E-cadherin alterations in familial breast cancer.

PMID 11305955 · PMC30704 · Breast cancer research : BCR · 2001 · 8 claims · 5 setups

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No pathogenic germline E-cadherin mutations were found in 19 familial breast cancer patients whose tumours showed LOH at the E-cadherin locus

blood same tumour pcr-sscp denaturing somatic
SNPs in cancer research and treatment.

PMID 14970847 · PMC2410167 · British journal of cancer · 2004 · 8 claims · 8 setups

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SNPs and haplotype-tagging SNPs (ht-SNPs) provide a resource for investigating genetic contributions to cancer susceptibility and outcome while reducing genotyping burden versus testing every SNP

lung bladder colon prostate candidate snp-based haplotype
Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

breast same selected hct116 expression methylation-specific rt-pcr
Discovering cancer genes by integrating network and functional properties.

PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups

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Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes

genes gene colon ppi pfam term
Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

PMID 41298871 · PMC12662399 · Nature cell biology · 2025 · 7 claims · 6 setups

Has reproduction · 100

S2-omics is an end-to-end workflow that automatically selects ROIs from H&E histology images to maximize molecular information content for spatial omics profiling.

gastric colorectal additional breast xenium visium histology
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
Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

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None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

breast quantitative fragment gene-expression
Mutations in the focal adhesion targeting region of deleted in liver cancer-1 attenuate their expression and function.

PMID 18829524 · PMC2597479 · Cancer research · 2008 · 8 claims · 6 setups

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The DLC-1 fragment spanning residues 201-500 is sufficient for focal adhesion targeting (FAT region)

a549 prostate colon mda-mb-468 immunofluorescence pcr colony
Failure to detect mutations in the retinoblastoma protein-binding domain of the transcription factor E2F-1 in human cancers.

PMID 9045954 · PMC5921028 · Japanese journal of cancer research : Gann · 1996 · 4 claims · 6 setups

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E2F-1 function is regulated by the RB protein through E2F-1's RB-binding domain, positioning E2F-1 downstream of RB

lung pancreatic stomach colon pcr-sscp
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

PMID 19820113 · PMC2808963 · Nucleic acids research · 2010 · 7 claims · 6 setups

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SelTarbase is a curated relational database of published mononucleotide-repeat mutation data from MSI-H human colorectal, gastric, endometrial tumors and colon cancer cell lines.

msi-h aggregated genome mnr sigmoid genome-wide
Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.

PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups

Has reproduction · 89

High pretreatment abundance of Lactobacillus (and Bifidobacterium) in gut microbiota correlates with absence of ACRIII in rectal cancer patients

fecal bacterial whole-abdomen cecal metagenomic random fecal

Experiments

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

MMASS: an optimized array-based method for assessing CpG island methylation.

Raf-1 activation disrupts its binding to keratins during cell stress.

Genomic and epigenetic instability in colorectal cancer pathogenesis.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

Low frequency of E-cadherin alterations in familial breast cancer.

SNPs in cancer research and treatment.

Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

Discovering cancer genes by integrating network and functional properties.

Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues.

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

Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

Mutations in the focal adhesion targeting region of deleted in liver cancer-1 attenuate their expression and function.

Failure to detect mutations in the retinoblastoma protein-binding domain of the transcription factor E2F-1 in human cancers.

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.