Table 1

Lists of seed nodes

User interested gene symbols

⟡ CEBPD (CCAAT/enhancer binding protein (C/EBP), delta)

⟡ SOD1(superoxide dismutase 1, soluble)

⟡ XRCC4 (X-ray repair complementing defective repair in Chinese hamster cells 4)

⟡ PTGS2 (prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase), (COX2))

⟡ RBMS3 (RNA binding motif, single stranded interacting protein)

⟡ STK39 (serine threonine kinase 39 (STE20/SPS1 homolog, yeast))

⟡ CUTL1 (cut-like homeobox 1)

⟡ CREG1 (cellular repressor of E1A-stimulated genes 1)

⟡ APBB2 (amyloid beta (A4) precursor protein-binding, family B, member 2)

⟡ ADAMTS1(ADAM metallopeptidase with thrombospondin type 1 motif, 1)

⟡ JAZF1(JAZF zinc finger 1)

⟡ JMJD2C (Jumonji domain 2)

⟡ MSI2 (musashi homolog 2 (Drosophila))

⟡ RABGAP1L (RAB GTPase activating protein 1-like)

⟡ NAV2 (neuron navigator 2)

⟡ ZMIZ1 (zinc finger, MIZ-type containing 1)

⟡ ZNF291 (SCAPER, S-phase cyclin A-associated protein in the ER)

⟡ ZRANB3 (zinc finger, RAN-binding domain containing 3)

⟡ CENTG2 (AGAP1, Homo sapiens ArfGAP with GTPase domain, ankyrin repeat and PH)

⟡ ATXN1 (ataxin 1-like)

⟡ THSD4 (thrombospondin, type I, domain containing 4)

⟡ CYP27C1 (cytochrome P450, family 27, subfamily C, polypeptide 1)


Resistance genes

⟡ IL1A (interleukin 1, alpha)

⟡ IL1B (interleukin 1, beta)

⟡ NFKB1 (nuclear factor of kappa light polypeptide gene enhancer in B-cells 1)

⟡ NFKB2 (nuclear factor of kappa light polypeptide gene enhancer in B-cells 2)

⟡ CDK4 (cyclin-dependent kinase 4)

⟡ MCM2 (minichromosome maintenance complex component 2)

⟡ MCM4 (minichromosome maintenance complex component 4)

⟡ CDC45L (CDC45 cell division cycle 45-like (S. cerevisiae))


DNA damage genes

⟡ MYC (v-myc myelocytomatosis viral oncogene homolog (avian))

⟡ TP53 (tumor protein p53)

⟡ PCNA (proliferating cell nuclear antigen)

⟡ TP73 (tumor protein p73)

⟡ ATF4 (activating transcription factor 4 (tax-responsive enhancer element B67))


Seed nodes were determined either by users' interesting genes [23] or were selected by biologists in advance. The criteria of selecting seed nodes are listed as follows: (i) genes with functional annotations such as 'DNA damage', 'DNA repair' [24], (ii) genes that are known transcription factors and are implicated in drug resistance [25], and (iii) genes that have been reported to have significantly altered expression patterns between platinum-based drugs chemosensitive and chemoresistant cells.

Chao et al. BMC Medical Genomics 2011 4:23   doi:10.1186/1755-8794-4-23

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