Table 1.

Functionally annotated gene categories from DAVID analysis of whole genome microarray results, comparing RCCs from responders to nonresponders

Functionally related group of genesaNumber of genes in submitted list/total number of genes in the category (%)PbBenjamini multiple comparison adjusted P
GO: mitochondrion72/1,087 (6.6)6.20E−132.32E−10
Swiss-Prot: mitochondrion57/832 (6.9)1.02E−114.02E−09
GO: coenzyme binding24/181 (13.3)1.19E−107.55E−08
GO: mitochondrial part45/595 (7.6)6.51E−101.22E−07
Swiss-Prot: oxidoreductase42/562 (7.5)6.89E−101.35E−07
GO: oxidation reduction47/639 (7.4)8.04E−111.62E−07
GO: cofactor binding26/249 (10.4)2.86E−099.08E−07
GO: organelle membrane63/1,096 (5.7)7.99E−099.96E−07
GO: mitochondrial envelope34/419 (8.1)2.35E−082.19E−06
Swiss-Prot: transit peptide34/476 (7.1)1.13E−071.11E−05
GO: mitochondrial membrane29/394 (7.4)2.25E−061.69E−04
GO: envelope38/622 (6.1)3.75E−062.00E−04
GO: organelle envelope38/620 (6.1)3.45E−062.15E−04
Swiss-Prot: endoplasmic reticulum40/713 (5.6)3.36E−062.64E−04
UniProt: transit peptide: mitochondrion33/467 (7.1)2.62E−073.06E−04
Swiss-Prot: nad18/189 (9.5)4.96E−063.25E−04
GO: mitochondrial inner membrane22/306 (7.2)7.10E−050.00265
GO: organelle inner membrane23/329 (7.0)7.05E−050.00292
GO: endoplasmic reticulum47/960 (4.9)6.68E−050.00312
Swiss-Prot: mitochondrion inner membrane16/193 (8.3)9.65E−050.00540
GO: acyl-CoA binding6/16 (37.5)3.17E−050.00670
GO: monovalent inorganic cation transmembranetransporter activity12/104 (11.5)5.26E−050.00833
GO: hydrogen ion transmembrane transporter activity11/90 (12.2)7.56E−050.00957
  • NOTE: Shown are functional gene categories upregulated in tumors from nonresponders and having a Benjamini adjusted P value (FDR) from DAVID of ≤0.010. The list submitted to DAVID contained 550 Illumina probe IDs for which the nonresponder/responder expression level fold change was ≥ 1.5 and the equal variance two-sided t test P value was ≤0.05. Gene groups are ordered according to the Benjamini adjusted P values.

  • aNomenclature as per DAVID web tool (https://david.ncifcrf.gov/).

  • bDAVID adjustment of the Fisher exact test (hypergeometric distribution) P value.