Table 3

Gene sets with strongest overlaps with observed differentially expressed genes.*

up-regulated gene sets

description

WC 3 h

WCCo 3 h

CoCl2 3 h

WC 3 d

WCCo 3 d

CoCl2 3 d



hypoxia related gene sets


HIF1_TARGETS

Hif-1 (hypoxia-inducible factor 1) transcriptional targets

0.17

0.01


HIFPATHWAY

BIOCARTA: Under normal conditions, HIF-1 is degraded; under hypoxic conditions, it activates transcription of genes controlled by hypoxic response elements (HREs)

0.02

0.20


HYPOXIA_FIBRO_UP

Up-regulated by hypoxia in normal fibroblasts from both young and old donors

0.20

0.65

0.05


HYPOXIA_NORMAL_UP

Up-regulated by hypoxia in normal, RPTEC renal cells

0.50

0.02


HYPOXIA_REG_UP

Up-regulated by hypoxia in renal cells, and down-regulated with reoxygenation

0.05

0.01

0.03


HYPOXIA_REVIEW

Genes known to be induced by hypoxia

0.22

0.75

0.00


MANALO_HYPOXIA_UP

Genes up-regulated in human pulmonary endothelial cells under hypoxic conditions or after exposure to AdCA5, an adenovirus carrying constitutively active hypoxia-inducible factor 1 (HIF-1alpha)

0.24

0.01

0.21


MENSE_HYPOXIA_UP

List of Hypoxia-induced genes found in both Astrocytes and HeLa Cell

0.00

0.02

0.13


RESPONSE_TO_HYPOXIA

GO:0001666. Change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension

0.12

0.08


carbohydrate metabolism


POLYSACCHARIDE_METABOLIC_PROCESS

GO:0005976. Chemical reactions and pathways involving polysaccharides, a polymer of more than 10 monosaccharide residues joined by glycosidic linkages

0.06


FRUCTOSE_AND_MANNOSE_METABOLISM

Genes involved in fructose and mannose metabolism

0.21

0.02


HSA00010_GLYCOLYSIS_AND_ GLUCONEOGENESIS

KEGG: Genes involved in glycolysis and gluconeogenesis

0.00

0.14


GLYCOGEN_METABOLISM

Genes involved in glycogen metabolism

0.04


GALACTOSE_METABOLISM

Genes involved in galactose metabolism

0.04


PENTOSE_PHOSPHATE_PATHWAY

Genes involved in pentose phosphate pathway

0.61

0.14


STARCH_AND_SUCROSE_ METABOLISM

Genes involved in starch and sucrose metabolism

0.01

0.50


endocrine metabolism


GN_CAMP_GRANULOSA_UP

Up-regulated in human granulosa cells by the gonadotropins LH and FSH, as well as by cAMP- stimulator forskolin

0.01

0.17


LH_GRANULOSA_UP

Up-regulated in human granulosa cells stimulated with luteinizing hormone (LH)

0.01


FSH_GRANULOSA_UP

Up-regulated in human granulosa cells stimulated with follicle stimulation hormone (FSH)

0.01


BREAST_CANCER_ESTROGEN_SIGNALING

Genes preferentially expressed in breast cancers, especially those involved in estrogen-receptor- dependent signal transduction

0.05


PROSTAGLANDIN_SYNTHESIS_ REGULATION

WIKIPATHWAYS: Prostaglandin Synthesis and Regulation

0.09


HSA04150_MTOR_SIGNALING_ PATHWAY

KEGG: Genes involved in mTOR signalling pathway

0.19


cell adhesion, structure, cytoskeleton


HSA04510_FOCAL_ADHESION

KEGG: Genes involved in focal adhesion

0.07

0.46


ACTIN_CYTOSKELETON

GO:0015629. Part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins

0.04


ACTIN_BINDING

GO:0003779. Interacting selectively with monomeric or multimeric forms of actin, including actin Filaments

0.06


CYTOSKELETON_DEPENDENT_ INTRACELLULAR_TRANSPORT

GO:0030705. The directed movement of substances along cytoskeletal elements such as microfilaments or microtubules within a cell

0.07


ANATOMICAL_STRUCTURE_FORMATION

GO:0048646. Process pertaining to the initial formation of an anatomical structure from unspecified parts

0.04


VASCULATURE_DEVELOPMENT

GO:0001944. Process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure

0.04


ANGIOGENESIS

GO:0001525. Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels

0.05


HSA04512_ECM_ RECEPTOR_INTERACTION

KEGG: Genes involved in ECM-receptor interaction

0.06

0.29


miscellaneous


G13_SIGNALING_PATHWAY

G13 signaling pathway

0.10

0.51


NUCLEOTIDE_BIOSYNTHETIC_PROCESS

GO:0009165. Chemical reactions and pathways resulting in the formation of nucleotides

0.09


CARBON_CARBON_LYASE_ACTIVITY

GO:0016830. Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond

0.10


ALKPATHWAY

Activin receptor-like kinase 3 (ALK3) is required during gestation for cardiac muscle development

0.29


CARDIACEGFPATHWAY

BIOCARTA: Cardiac hypertrophy, a response to high blood pressure, is stimulated by GPCR ligands such as angiotensin II that activate the EGF pathway

0.21

0.01


WNT_SIGNALING

Wnt signaling genes

0.01


HSA05211_RENAL_CELL_CARCINOMA

Genes involved in renal cell carcinoma

0.07


NKTPATHWAY

BIOCARTA: T cell differentiation into Th1 and Th2 cells occurs by differential chemokine receptor expression, which mediates tissue localization and immune response

0.29


BIOGENIC_AMINE_SYNTHESIS

WIKIPATHWAYS: Genes involved in synthesis of biogenic amines

0.23


HSA00591_LINOLEIC_ACID_METABOLISM

Genes involved in linoleic acid metabolism

0.22


HSA00361_GAMMA_HEXACHLOROCYCLOHEXANE_DEGRADATION

KEGG: Genes involved in gamma-hexachlorocyclohexane degradation

0.17


down-regulated gene sets

description

WC 3 h

WCCo 3 h

CoCl2 3 h

WC 3 d

WCCo 3 d

CoCl2 3 d


RNA metabolism and processing


MRNA_METABOLIC_PROCESS

GO:0016071. Chemical reactions and pathways involving mRNA

0.23


RIBONUCLEOPROTEIN_COMPLEX_

GO:0022613. The cellular process by which a complex containing RNA and proteins, is synthesized,

0.25


BIOGENESIS_AND_ASSEMBLY

aggregates, and bonds together


RNA_PROCESSING

GO:0006396. Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules

0.20


RNA_SPLICING__VIA_TRANSESTERIFICATION_ REACTIONS

GO:0000375. Splicing of RNA via a series of two transesterification reactions

0.20


SEQUENCE_SPECIFIC_ DNA_BINDING

GO:0043565. Interacting selectively with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding

0.33


TRNA_METABOLIC_PROCESS

GO:0006399. Chemical reactions and pathways involving tRNA

0.27


nucleus and the nuclear membrane related gene sets


PORE_COMPLEX

GO:0046930. Any small opening in a membrane that allows the passage of gases and/or liquids.

0.28


NUCLEAR_PORE

GO:0005643. Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined

0.19


NUCLEAR_LUMEN

GO:0031981. The volume enclosed by the nuclear inner membrane

0.31


NUCLEAR_MEMBRANE

GO:0031965. Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space

0.31


enzyme and receptor activity


UBIQUITIN_PROTEIN_ LIGASE_ACTIVITY

GO:0004842. Catalysis of the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine

0.32


SMALL_PROTEIN_CONJUGATING_ ENZYME_ACTIVITY

GO:0008639. Catalysis of the covalent attachment of small proteins, such as ubiquitin or ubiquitin-like proteins, to lysine residues on a target protein. This function may be performed alone or in conjunction with an E3, ubiquitin-like protein ligase

0.21


CASPASEPATHWAY

BIOCARTA: Caspases are cysteine proteases active in apoptosis

0.30


* identified by GSEA (gene set enrichment analysis), using the databases MSigDB C2 and C5; number of entries is limited to gene sets with a false discovery rate (FDR) < 0.35 in at least one of the treatments and FDR < 0.1 for the WC-Co 3 d treatment; only gene sets obviously related to biochemical pathways or cellular organelles were selected; full table provided as Additional File 3

Busch et al. BMC Genomics 2010 11:65   doi:10.1186/1471-2164-11-65

Open Data