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 | ||||