Table 1

GEO Datasets Used for Testing

DataSet

Title

Organism


GDS3505

Seedling roots response to auxin and ethylene availability

Arabidopsis thaliana

GDS3521

Retina response to hypoxia and subsequent reoxygenation: time course

Mus musculus

GDS3538

Age and diet effect on canine skeletal muscles

Canis lupus familiaris

GDS3561

Occupational benzene exposure: peripheral blood mononuclear cells (HumanRef-8)

Homo sapiens

GDS3579

Fer-1 null mutants

Caenorhabditis elegans

GDS3592

Ovarian normal surface epithelia and ovarian cancer epithelial cells

Homo sapiens

GDS3595

Macrophage response to H1N1 and H5N1 influenza viral infections

Homo sapiens

GDS3603

Renal cancer response to rapamycin analog CCI-779 treatment:

Homo sapiens

GDS3605

Spared nerve injury model of peripheral neuropathic pain: dorsal horn of spinal cord

Rattus norvegicus

GDS3610

Nasopharyngeal carcinoma

Homo sapiens

GDS3622

Nrf2-deficient lung response to cigarette smoke: dose response and time course

Mus musculus

GDS3623

Heart regeneration in zebrafish

Danio rerio

GDS3639

Male and female fruit flies of various wild-type laboratory strains

Drosophila melanogaster

GDS3640

Copper effect on liver cell line: dose response and time course

Homo sapiens

GDS3644

Cerebral palsy: wrist muscles

Homo sapiens

GDS3646

Celiac disease: primary leukocytes

Homo sapiens

GDS3648

Cardiomyocyte response to various types of fatty acids in vitro

Rattus norvegicus

GDS3661

Hypertensive heart failure model

Rattus norvegicus

GDS3672

Hypertension model: aorta

Mus musculus

GDS3690

Atherosclerotic Coronary Artery Disease: circulating mononuclear cell types

Homo sapiens

GDS3715

Insulin effect on skeletal muscle

Homo sapiens

GDS3716

Breast cancer: histologically normal breast epithelium

Homo sapiens

GDS3703

Addictive drugs effect on brain striatum: time course

Mus musculus

GDS3707

Acute ethanol exposure: time course

Drosophila melanogaster

GDS3692

Lean B6.C-D7Mit353 strain: various tissues

Mus musculus


The 25 datasets obtained from the Gene Expression Omnibus (GEO) [25]. All datasets were retrieved between 4-04-2011 and 4-23-2011. Each dataset was log-transformed if it had not been already. For each dataset, four different correlation thresholds were used to build unweighted graphs.

Eblen et al. BMC Bioinformatics 2012 13(Suppl 10):S5   doi:10.1186/1471-2105-13-S10-S5

Open Data