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 29

System / cell line: muscle ✕ Assay: profiling ✕ Clear

Sources of variability and effect of experimental approach on expression profiling data interpretation.

PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

Full-text index only

Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

skeletal muscle spleen myogenic affymetrix duplicate unsupervised
Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism.

PMID 31825657 · PMC7099524 · American journal of physiology. Cell physiology · 2020 · 8 claims · 8 setups

Has reproduction · 64

L6, C2C12, and primary human myotubes show substantial heterogeneity in transcriptomic and metabolic profiles

c2c12 transcriptomic proliferation brdu
Genetics and functional genomics of type 2 diabetes mellitus.

PMID 14659011 · PMC329413 · Genome biology · 2003 · 7 claims · 5 setups

Full-text index only

Genome-wide transcription profiling of diabetic skeletal muscle reveals coordinated downregulation of oxidative phosphorylation genes, converging on PGC1α as a central regulator.

skeletal population microarray real-time genetic
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

Full-text index only

Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls

activated skeletal muscle altered affymetrix quantitative sirna
Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

Full-text index only

Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

liver atherosclerotic 128-gene independent two-way gene bioinformatic
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

Full-text index only

Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

lms independent soft gene array immunohistochemistry
Genomic and proteomic profiling of responses to toxic metals in human lung cells.

PMID 12760830 · PMC1241504 · Environmental health perspectives · 2003 · 8 claims · 8 setups

Full-text index only

Toxic metals (Cd, Cr, Ni, As) each induce a largely distinct, metal-specific pattern of gene expression changes in BEAS-2B human bronchial epithelial cells

beas-2b cdna western kinetworks
In silico promoters: modelling of cis-regulatory context facilitates target predictio.

PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

Full-text index only

An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

serca2 rantes genes podocyte-associated literature-based promoter cross-referenced
Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

Full-text index only

A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

lsl-krasg12d soft combined mfh microarray gene oncogenic
MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups

Full-text index only

High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status

high ovarian mir-29a mirna unsupervised significance
Applying proteomics to the diagnosis and treatment of ALS and related diseases.

PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

Full-text index only

Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

csf spinal biofluid muscle 2d-dige antibody luminex
TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 6 claims · 4 setups

Has reproduction · 84

TransOrGAN can infer transcriptomic profiles between any 2 of 9 organs with an average cosine similarity of 0.984 between synthetic and real profiles

fischer transcriptomic bulk gan-based toxicity
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

Full-text index only

Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
Genomics in space life sciences.

PMID 18558380 · PMC5054090 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 6 setups

Full-text index only

Sudden changes in gravity alter mRNA levels of various genes, indicating molecular-level effects of microgravity

keratinocyte wi-38 candida rice microarray suppression pathogenicity
Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

PMID 20006904 · PMC2814002 · Neuropeptides · 2010 · 8 claims · 5 setups

Full-text index only

Bioinformatic survey of chicken genome/EST/HTGS databases identifies previously unreported chicken neuropeptide genes

chicken blast microarray est
The mitochondrial genome, a growing interest inside an organelle.

PMID 18488415 · PMC2526360 · International journal of nanomedicine · 2008 · 8 claims · 8 setups

Full-text index only

mtDNA mutations are causally linked to a wide range of mitochondrial diseases, aging, and chronic degenerative diseases

post-mitotic mtdna homozygous high-fat southern rflp-pcr dhplc
Organismal complexity, cell differentiation and gene expression: human over mouse.

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

Full-text index only

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
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.

PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 7 setups

Has reproduction · 97

TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.

aortic brown genes training wgcna biological gsva

Experiments

Sources of variability and effect of experimental approach on expression profiling data interpretation.

Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism.

Genetics and functional genomics of type 2 diabetes mellitus.

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

Inferring combinatorial regulation of transcription in silico.

Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Genomic and proteomic profiling of responses to toxic metals in human lung cells.

In silico promoters: modelling of cis-regulatory context facilitates target predictio.

Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

Applying proteomics to the diagnosis and treatment of ALS and related diseases.

TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

Genomics in space life sciences.

Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

The mitochondrial genome, a growing interest inside an organelle.

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

Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.