Skip to main content

Table 1 Lists of seed nodes

From: An integrative approach to identifying cancer chemoresistance-associated pathways

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))
  1. 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.