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 32

System / cell line: tissues ✕ Assay: promoter ✕ Clear

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

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RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite
Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

PMID 18475302 · PMC2391125 · British journal of cancer · 2008 · 7 claims · 5 setups

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RUNX3 promoter hypermethylation is frequent in primary pancreatic cancer tissue

pancreatic microsatellite methylation-specific bisulphite
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

PMID 16381948 · PMC1347397 · Nucleic acids research · 2006 · 6 claims · 2 setups

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CAGE Basic and Analysis Databases together form a comprehensive resource for promoter analysis using CAGE tag data from human and mouse

tested cage race
A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 6 claims · 8 setups

Has reproduction · 76

Hnf4a is a major transcriptional regulator of Dnajc22.

mus tissues liver-specific kidney bulk microarray chip-seq
Adaptively inferring human transcriptional subnetworks.

PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

liver proximal hela predicted microarray computational novo
Genome Network and FANTOM3: assessing the complexity of the transcriptome.

PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

fantom3 genome large-scale mammalian cage full-length genome
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

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Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq
'Genome design' model and multicellular complexity: golden middle.

PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

normal genes proteins encoded oligonucleotide gene functional
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

putative nonredundant homo genes computational pssm semantic
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

normal dld1 beas2b ramos tss comparative
Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 6 claims · 7 setups

Has reproduction · 62

Combining four de novo models (PWM, diPWM, BaMM, InMoDe) significantly increases the fraction of recognized peaks versus PWM alone (by 26.3%).

hg38 foxa2 pwm whole-genome chip-seq pwm dipwm
Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

Has reproduction

Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics
Human epigenome project--up and running.

PMID 14691553 · PMC300691 · PLoS biology · 2003 · 7 claims · 4 setups

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Epigenetic modifications (e.g., DNA methylation) rather than DNA sequence differences explain phenotypic differences between genetically identical individuals, such as monozygotic twins or inbred mice.

expressed bat8 genetically methylation genome-wide phenotypic
Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups

Has reproduction · 70

AR enhancer/chromatin binding usage is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites shared by half of tumors analyzed.

prostate normal ar+ pca chip-seq rna-seq massively
Organismal complexity, cell differentiation and gene expression: human over mouse.

PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

human-mouse oligonucleotide exon comparative
Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

Has reproduction · 88

Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

arabidopsis deg promoter selected meta-analysis transcription hexamer
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

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MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

Adaptively inferring human transcriptional subnetworks.

Genome Network and FANTOM3: assessing the complexity of the transcriptome.

Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

'Genome design' model and multicellular complexity: golden middle.

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

Human epigenome project--up and running.

Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

Organismal complexity, cell differentiation and gene expression: human over mouse.

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.