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Table 3 Genes included in each cluster

From: Different responses to oxidized low-density lipoproteins in human polarized macrophages

Cluster A.
Gene Symbol Ref Seq ID M0 M1 M2 NCBI official full name
CHI3L2 NM_004000 1.170712 0.008113 -0.453072 chitinase 3-like 2
PARP8 NM_024615 1.018767 0.147437 -0.206628 poly (ADP-ribose) polymerase family, member 8
MAP4K4 NM_145686 1.115230 -0.302140 -0.763189 mitogen-activated protein kinase kinase kinase kinase 4
CD44 NM_001001391 1.312520 -0.201936 -0.048693 CD44 molecule
CYP27B1 NM_000785 1.111109 -0.055705 -0.015432 cytochrome P450, family 27, subfamily B, polypeptide 1
SLC1A2 NM_004171 1.466166 -0.088519 0.225126 solute carrier family 1 (glial high affinity glutamate transporter), member 2
CKMT1 NM_020990 1.436353 0.264923 0.338353 creatine kinase, mitochondrial 1B
MYOD1 NM_002478 1.665245 0.211625 0.330158 myogenic differentiation 1
CD40 NM_001250 1.319905 -0.606033 0.379319 CD40 molecule, TNF receptor superfamily member 5
PRKAR2B NM_002736 1.349370 -0.472458 0.347752 protein kinase, cAMP-dependent, regulatory, type II, beta
KIAA0913 NM_015037 1.244477 -0.318545 0.447287 KIAA0913
SNX10 NM_013322 1.138265 -0.351416 0.635676 sorting nexin 10
HHIP NM_022475 1.177555 -0.537186 0.506197 hedgehog interacting protein
BIRC3 NM_001165 1.499122 -0.583781 -0.065715 baculoviral IAP repeat-containing 3
ZBTB7C NM_001039360 1.293925 -1.001009 0.404020 zinc finger and BTB domain containing 7C
PACRGL NM_145048 2.026548 -0.460488 0.187722 PARK2 co-regulated-like
CCL23 NM_005064 2.471357 -0.192407 -0.036793 chemokine (C-C motif) ligand 23
Cluster B.
Gene Symbol Ref Seq ID M0 M1 M2 NCBI official full name
NDN NM_002487 -0.169667 1.457695 -0.617320 necdin homolog (mouse)
FAM129C NM_173544 -0.110208 1.321559 -0.841954 family with sequence similarity 129, member C
NME6 NM_005793 -0.315804 1.345342 -0.759802 non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)
TMEM99 NM_145274 -0.390527 1.497197 -0.676125 transmembrane protein 99
ATP2B1 NM_001682 -0.371182 1.535878 -0.824423 ATPase, Ca++ transporting, plasma membrane 1
KIF1A NM_004321 -0.362399 1.333531 -0.928733 kinesin family member 1A
TMEM188 NM_153261 -0.375073 1.157188 -0.955238 transmembrane protein 188
PLEKHG4 NM_015432 -0.414580 1.052587 -0.706013 pleckstrin homology domain containing, family G (with RhoGef domain) member 4
NOXA1 NM_006647 -0.322207 1.015456 -0.592170 NADPH oxidase activator 1
CUX1 NM_001913 -0.236206 1.147118 -0.551592 cut-like homeobox 1
SBNO2 NM_014963 -0.294540 1.271977 -0.630553 strawberry notch homolog 2 (Drosophila)
TIGD5 NM_032862 -0.376362 1.224225 -0.526717 tigger transposable element derived 5
CTSL2 NM_001333 -0.428772 1.153800 -0.359408 cathepsin L2
ZNF24 NM_006965 -0.385988 1.069071 -0.360632 zinc finger protein 24
STK32C NM_173575 -0.634840 1.124350 -0.544619 serine/threonine kinase 32C
NUDT17 NM_001012758 -0.524910 1.111636 -0.519731 nudix (nucleoside diphosphate linked moiety X)-type motif 17
CALML4 NM_033429 -0.433422 1.089113 -0.492229 calmodulin-like 4
C7orf33 NM_145304 -0.435642 1.106760 -0.512504 chromosome 7 open reading frame 33
FBXO22 NM_012170 -0.203452 1.309369 -0.481216 F-box protein 22
LINGO1 NM_032808 -0.174931 1.312372 -0.445152 leucine rich repeat and Ig domain containing 1
ZMYND19 NM_138462 -0.243665 1.351306 -0.517691 zinc finger, MYND-type containing 19
CCR1 NM_001295 -0.165232 1.419892 -0.480175 chemokine (C-C motif) receptor 1
ATRX NM_000489 -0.498685 1.285463 -0.371568 alpha thalassemia/mental retardation syndrome X-linked
FRMD4B NM_015123 -0.477381 1.252296 -0.287931 FERM domain containing 4B
CEP164 NM_014956 -0.419638 1.269277 -0.283263 centrosomal protein 164kDa
LANCL2 NM_018697 -0.393507 1.324253 -0.242555 LanC lantibiotic synthetase component C-like 2 (bacterial)
UBA5 NM_024818 -0.478021 1.390785 -0.479541 ubiquitin-like modifier activating enzyme 5
GGCX NM_000821 -0.380201 1.330677 -0.476370 gamma-glutamyl carboxylase
FOXN3 NM_005197 -0.772837 1.196028 -0.268613 forkhead box N3
TP53BP1 NM_005657 -0.797822 1.249895 -0.460222 tumor protein p53 binding protein 1
ORC6 NM_014321 -0.633454 1.305326 -0.322922 origin recognition complex, subunit 6
ST7 NM_018412 -0.678132 1.309238 -0.290689 suppression of tumorigenicity 7
OGFOD1 NM_018233 0.061541 1.413933 -0.438702 2-oxoglutarate and iron-dependent oxygenase domain containing 1
UBE2B NM_003337 0.146284 1.431435 -0.295974 ubiquitin-conjugating enzyme E2B (RAD6 homolog)
GALNTL4 NM_198516 0.178950 1.470650 -0.270045 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4
HSPA14 NM_016299 0.185892 1.419392 -0.264205 heat shock 70kDa protein 14
PEX13 NM_002618 0.137507 1.527385 -0.274508 peroxisomal biogenesis factor 13
ATP2B2 NM_001001331 0.084953 1.689567 -0.394052 ATPase, Ca++ transporting, plasma membrane 2
TAAR2 NM_014626 0.168770 1.695874 -0.439255 trace amine associated receptor 2
HUS1 NM_004507 0.098273 1.666199 -0.226370 HUS1 checkpoint homolog (S. pombe)
RIC8B NM_018157 0.214093 1.650594 -0.307883 resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)
DNAJC17 NM_018163 0.172153 1.482705 -0.492935 DnaJ (Hsp40) homolog, subfamily C, member 17
TMEM130 NM_152913 0.206368 1.399311 -0.480833 transmembrane protein 130
AP2A2 NM_012305 0.285524 1.391232 -0.458091 adaptor-related protein complex 2, alpha 2 subunit
TTTY13 NR_001537 0.381981 1.560081 -0.451429 testis-specific transcript, Y-linked 13 (non-protein coding)
AKT1S1 NM_032375 0.385837 1.517956 -0.371995 AKT1 substrate 1 (proline-rich)
WNT3 NM_030753 0.009319 1.560600 -0.801987 wingless-type MMTV integration site family, member 3
ZNF443 NM_005815 0.154517 1.457293 -0.742146 zinc finger protein 443
TFCP2L1 NM_014553 0.207710 1.525949 -0.955561 transcription factor CP2-like 1
KIAA0355 NM_014686 0.278629 1.724807 -0.576470 KIAA0355
ASAP2 NM_003887 0.524513 1.733462 -0.459752 ArfGAP with SH3 domain, ankyrin repeat and PH domain 2
C14orf49 NM_152592 0.578042 1.624871 -0.365254 chromosome 14 open reading frame 49
NFKB2 NM_002502 0.652839 1.882528 -0.343188 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)
ZNF586 NM_017652 0.328381 1.848104 -0.284595 zinc finger protein 586
RNMTL1 NM_018146 0.277170 1.645924 -0.133286 RNA methyltransferase like 1
FOSL2 NM_005253 0.386974 1.569486 -0.229451 FOS-like antigen 2
SATB1 NM_002971 0.542138 1.252296 -0.749110 SATB homeobox 1
ASB6 NM_177999 0.666548 1.536652 -0.584820 ankyrin repeat and SOCS box-containing 6
SLC5A3 NM_006933 0.682674 1.388148 -0.424733 solute carrier family 5 (sodium/myo-inositol cotransporter), member 3
C8orf84 NM_153225 0.637255 1.709652 -0.981619 chromosome 8 open reading frame 84
MON1B NM_014940 0.234404 2.712191 -0.753618 MON1 homolog B (yeast)
PIGO NM_152850 0.134053 2.574539 -0.004491 phosphatidylinositol glycan anchor biosynthesis, class O
STAM NM_003473 -0.221822 2.697280 -0.150394 signal transducing adaptor molecule (SH3 domain and ITAM motif) 1
CCDC45 NM_138363 -0.046055 2.118025 -0.312274 coiled-coil domain containing 45
GYS1 NM_002103 -0.699205 1.685994 -0.629003 glycogen synthase 1 (muscle)
RENBP NM_002910 -0.403657 1.957579 -0.580833 renin binding protein
BTD NM_000060 -0.348646 1.647239 -0.685758 biotinidase
FAM172A NM_032042 -0.409833 1.717425 -0.665763 family with sequence similarity 172, member A
PIK3R4 NM_014602 -0.188899 2.325311 -0.729078 phosphoinositide-3-kinase, regulatory subunit 4
RSAD1 NM_018346 -0.251002 2.260460 -0.748812 radical S-adenosyl methionine domain containing 1
ZNF626 NM_145297 -0.252970 1.842391 -0.910235 zinc finger protein 626
CTH NM_001902 -1.060839 2.365953 -1.038817 cystathionase (cystathionine gamma-lyase)
Cluster C.
Gene Symbol Ref Seq ID M0 M1 M2 NCBI official full name
MXD3 NM_031300 -0.800223 0.116059 1.984245 MAX dimerization protein 3
CD14 NM_000591 -1.193454 -0.266058 2.053786 CD14 molecule
BARX1 NM_021570 -1.650218 0.236670 1.728783 BARX homeobox 1
ZNF331 NM_018555 -1.729498 -0.028187 1.786943 zinc finger protein 331
GPR54 NM_032551 -0.085064 -0.929503 1.669680 KISS1 receptor
ANP32A NM_006305 -0.155917 -0.929503 1.827632 acidic (leucine-rich) nuclear phosphoprotein 32 family, member A
C19orf54 NM_198476 -0.205921 -0.803972 1.634746 chromosome 19 open reading frame 54
G0S2 NM_015714 -0.367904 -0.858834 2.131860 G0/G1switch 2
SPATA3 NM_139073 -0.301818 -0.432004 1.766064 spermatogenesis associated 3
FOXA2 NM_153675 -0.306075 -0.533883 1.983144 forkhead box A2
PSORS1C2 NM_014069 -0.423428 -0.713119 1.449567 psoriasis susceptibility 1 candidate 2
SNN NM_003498 -0.492216 -1.239138 1.185086 stannin
CDKN2B NM_078487 -0.404103 -0.847300 1.024029 cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)
ZNF257 NM_033468 -0.916132 -1.388935 1.189490 zinc finger protein 257
ZBTB4 NM_020899 -0.296438 -1.533325 0.937391 zinc finger and BTB domain containing 4
CASP2 NM_032983 -1.527530 -0.751505 1.026536 caspase 2, apoptosis-related cysteine peptidase
TCTEX1D1 NM_152665 -1.661006 -0.348442 1.280638 Tctex1 domain containing 1
FILIP1L NM_014890 -0.967885 -0.212315 1.018932 filamin A interacting protein 1-like
USP52 NM_014871 -0.885665 -0.310932 1.097774 PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)
SETD8 NM_020382 -1.020324 -0.599401 0.697655 SET domain containing (lysine methyltransferase) 8
C13orf31 NM_153218 -1.442594 -0.330041 0.688789 chromosome 13 open reading frame 31
POLD1 NM_002691 -1.311086 -0.314006 0.812769 polymerase (DNA directed), delta 1, catalytic subunit 125kDa
DNMT3A NM_022552 -1.207327 -0.289399 0.489584 DNA (cytosine-5-)-methyltransferase 3 alpha
TGFBI NM_000358 -1.324217 -0.324120 0.308245 transforming growth factor, beta-induced, 68kDa
ANP32C NM_012403 -1.493138 -0.380761 0.494101 acidic (leucine-rich) nuclear phosphoprotein 32 family, member C
ITGA2B NM_000419 -1.109218 0.018385 1.026536 integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)
RGS3 NM_130795 -1.022299 -0.038087 0.656812 regulator of G-protein signaling 3provided
MARCH1 NM_017923 -1.374411 0.233896 0.729622 membrane-associated ring finger (C3HC4) 1provided
The top functional ontology categories  
Cluster A. P -value
   Cell-mediated Immune Response 9.46E-06-2.65E-02
   Cellular Movement 9.46E-06-3.76E-02
   Hematological System Development and Function 9.46E-06-3.57E-02
   Immune Cell Trafficking 9.46E-06-2.49E-02
   Cardiovascular Disease 2.64E-05-3.76E-02
Cluster B. P -value
   Cell Cycle 1.31E-04-3.28E-02
   Cell Cycle 1.31E-04-3.28E-02
   DNA Replication, Recombination, and Repair 1.31E-04-4.51E-02
   Gene Expression 2.16E-03-3.35E-02
   Cellular Development 3.51E-03-3.64E-02
   Nervous System Development and Function 3.51E-03-4.7E-02
Cluster C. P -value
   Carbohydrate Metabolism 1.12E-04-4.09E-02
   Lipid Metabolism 1.12E-04-4.09E-02
   Small Molecule Biochemistry 1.12E-04-4.09E-02
   Cell Death 3.76E-04-4.81E-02
   Nervous System Development and Function 7.79E-04-3.33E-02
  1. Three clusters were extracted from the heat map shown in Figure 5. There were 17, 72, and 28 annotated genes in clusters A, B, and C, respectively. The top functional ontology categories and the corresponding P-values in each subset are shown. NFKB2 and PIK3R4 were found in cluster B. The values denote fold changes (log2 ratio) of normalized intensities during oxLDL treatment.