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Table 4 Genes differentially expressed in lobular versus ductal invasive carcinomas by rank products and/or pairwise analysis

From: Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis

Probe Set1 Gene Symbol Gene Title Rank products Pairwise comparison
    Fold-change Incr/Decr
Cell adhesion
201131_s_at CDH1 Cadherin 1, type 1, E-cadherin (epithelial) -6.0 3/19
207169_x_a DDR1 Discoidin domain receptor family, member 1 n 5/19
204776_at THBS4 Thrombospondin 4 n 19/2
219087_at ASPN Asporin (LRR class 1) 3.9 23/0
Wnt signalling
223168_at RHOU RAS homolog gene family, member U n 2/20
203230_at DVL1 Dishevelled, dsh homolog 1 (Drosophila) n 20/0
Protein ubiquitination
215392_at USP3 Ubiquitin specific peptidase 3 -5.0 1/21
218247_s_at RKHD2 Ring finger and KH domain containing 2 -4.6 0/19
1569472_s_at TTC3 Tetratricopeptide repeat domain 3 -4.5 0/23
Regulation of transcription
226115_at AHCTF1 AT hook containing transcription factor 1 -4.0 0/22
201587_s_at IRAK1 Interleukin-1 receptor-associated kinase 1 n 2/19
202599_s_at NRIP1 Nuclear receptor interacting protein 1 n 0/19
201773_at ADNP Activity-dependent neuroprotector n 0/20
203637_s_at MID1 Midline 1 (Opitz/BBB syndrome) 4.0 20/0
235444_at FOXP1 Forkhead box P1 n 19/4
Electron and protein transport
204351_at S100P S100 calcium binding protein P -5.3 0/19
225177_at RAB11FIP1 RAB11 family interacting protein 1 (class I) -3.5 2/21
204041_at MAOB Monoamine oxidase B 3.5 20/4
212902_at SEC24A SEC24 related gene family, member A 3.5 19/2
Cell cycle regulation, cell proliferation and signaling
204170_s_at CKS2 CDC28 protein kinase regulatory subunit 2 -4.8 2/20
207414_s_at PCSK6 Proprotein convertase subtilisin/kexin type 6 n 4/19
209678_s_at PRKCI Protein kinase C, iota n 0/22
209817_at PPP3CB Protein phosphatase 3, catalytic subunit, beta isoform (calcineurin A beta) n 0/24
201324_at EMP1 Epithelial membrane protein 1 n 21/0
Metabolism and enzyme activity
205509_at CPB1 Carboxypeptidase B1 (tissue) -11.1 0/19
223746_at STK4 Serine/threonine kinase 4 -4.5 2/20
225491_at SLC1A2 Solute carrier family 1 (glial high affinity glutamate transporter), member 2 -4.1 0/20
211379_x_at B3GALT3 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 -4.0 0/20
219073_s_at OSBPL10 Oxysterol binding protein-like 10 -4.0 1/21
229366_at CRBN Cereblon -3.6 0/20
226350_at CHML Choroideremia-like (Rab escort protein 2) n 0/24
217717_s_at YWHAB Tyrosine 3-monooxygenase/tryptophan 5-mono-oxygenase activation protein, beta polypeptide n 1/20
49452_at ACACB Acetyl-Coenzyme A carboxylase beta n 19/0
220770_s_at LOC63920 Transposon-derived Buster3 transposase-like 5.3 24/0
Actin and cytoskeletal protein binding
211776_s_at EPB41L3 Erythrocyte membrane protein band 4.1-like 3 -5.3 0/21
201341_at ENC1 Ectodermal-neural cortex (with BTB-like domain) n 19/3
Nuclear components
218585_s_at DTL Denticleless homolog (Drosophila) -4.6 1/19
225706_at GLCCI1 Glucocorticoid induced transcript 1 -4.5 0/25
241863_x_at TTC14 Tetratricopeptide repeat domain 14 -4.4 1/20
228069_at FAM54A Family with sequence similarity 54, member A -3.8 0/20
208576_s_at HIST1H3B Histone 1, H3b -3.3 1/19
Other
1568838_at --- ↓ Full-length cDNA clone CS0DF033YE17 of Fetal brain of Homo sapiens (human) -5.0 1/20
226067_at C20orf114 Chromosome 20 open reading frame 114 -4.9 0/19
1553979_at --- ↓ Homo sapiens, clone IMAGE:3906992, mRNA -4.1 0/19
230534_at MGC15634 Hypothetical protein MGC15634 -3.6 2/20
226671_at --- ↓ CDNA clone IMAGE:4797120 -3.8 2/20
219768_at VTCN1 V-set domain containing T cell activation inhibitor 1 7.8 21/2
214657_s_at TncRNA Trophoblast-derived noncoding RNA 4.5 21/0
213004_at ANGPTL2 Angiopoietin-like 2 n 19/4
  1. ↑ – upregulated in lobular carcinoma; ↓ – downregulated in lobular carcinoma; n – gene not found by rank products at the level of 10% of false positives, Incr/decr – increase or decrease in lobular versus ductal carcinoma by pairwise comparison.
  2. 1All 32 probe sets identified by combined pairwise comparison and rank products are included, also a number of genes found by pairwise comparison were validated by immunohistochemistry (DVL1, DDR1, EMP1), therefore, functional categories also include named genes identified by pairwise analysis.