Table 1.
Differentially expressed genes (DEGs)
| Symbol | Gene Name | Fold Change | ||
|---|---|---|---|---|
| Day 3 | Day 6 | |||
| Apoptosis | ||||
| BE112895 | Pea15 * | phosphoprotein enriched in astrocytes 15 | 2.55 | |
| AI411997 | Adamtsl4 | ADAMTS-like 4 | 1.90 | |
| NM_012935 | Cryab | crystallin, alpha B | 1.75 | |
| NM_022546 | Dapk3 | death-associated protein kinase 3 | 1.51 | 1.54 |
| BF282636 | RGD1305457 | similar to RIKEN cDNA 1700023M03 | 1.54 | |
| NM_017180 | Phlda1 | pleckstrin homology-like domain, family A, member 1 | 1.50 | |
| Cell Adhesion | ||||
| Z78279 | Col1a1 | collagen, type 1, alpha 1 | 7.68 | 14.09 |
| AF056034 | Nexn | nexilin | 4.77 | 4.55 |
| BI303379 | Tnfrsf12 | tumor necrosis factor receptor superfamily, member 12a | 3.70 | 4.21 |
| BF407194 | Itgb1bp2 * | integrin beta 1 binding protein 2 | 2.14 | 2.09 |
| NM_030828 | Gpc1 | glypican 1 | 2.02 | |
| NM_017022 | Itgb1 | integrin beta 1 | 1.82 | |
| NM_012811 | Mfge8 | milk fat globule-EGF factor 8 protein | 1.79 | |
| BG379319 | Tgfbi | transforming growth factor, beta induced | 1.72 | |
| NM_022266 | Ctgf | connective tissue growth factor | 1.66 | |
| AW433888 | Vcl * | vinculin | 1.63 | |
| NM_133409 | Ilk | integrin linked kinase | 1.52 | 1.61 |
| BI275904 | Lims2 * | LIM and senescent cell antigen like domains 2 | 1.63 | 1.59 |
| AI008975 | LOC311772 | similar to nidogen 2 | 1.57 | |
| NM_022523 | Cd151 | CD151 antigen | 1.51 | |
| NM_019237 | Pcolce | procollagen C-proteinase enhancer protein | 1.50 | |
| AB001382 | Spp1 | secreted phosphoprotein 1 | 2.10 | |
| NM_012774 | Gpc3 | glypican 3 | 1.87 | |
| Cell Structure and Motility | ||||
| U22520 | Cxcl10 | chemokine (C-X-C motif) ligand 10 | 3.66 | |
| BE111697 | Kif20a * | kinesin family member 20A | 3.55 | |
| NM_022531 | Des | desmin | 1.85 | 3.29 |
| NM_031005 | Actn1 | actinin, alpha 1 | 3.00 | 3.19 |
| BI283060 | Flna * | filamin, alpha | 2.60 | 2.96 |
| NM_019131 | Tpm1 | tropomyosin 1, alpha | 3.33 | 2.90 |
| BI279044 | Myl9 * | myosin, light polypeptide 9, regulatory | 5.58 | 2.81 |
| AI179391 | Enh | enigma homolog | 2.04 | 2.58 |
| NM_017148 | Csrp1 | cysteine and glycine-rich protein 1 | 1.92 | 2.42 |
| X03369 | Tubb2b | tubulin, beta 2b | 2.34 | |
| BI274903 | RGD1305887 * | similar to RIKEN cDNA 2310057H16 | 1.80 | 2.27 |
| AA012755 | MGC109519 | similar to tropomyosin 1, embryonic fibroblast - rat | 2.23 | |
| NM_019361 | Arc | activity regulated cytoskeletal-associated protein | 2.18 | |
| NM_012987 | Nes | nestin | 2.07 | |
| AI598442 | RGD1564875 * | similar to mKIAA0613 protein | 2.04 | |
| AW919109 | Cap2 | CAP, adenylate cyclase-associated protein, 2 (S. cerevisiae) | 1.88 | 2.03 |
| BI285440 | Tubb5 | tubulin, beta 5 | 1.91 | |
| AI103106 | Lmnb1 | lamin B1 | 1.86 | |
| AA892044 | Tubb2 | tubulin, beta, 2 | 1.80 | |
| NM_013194 | Myh9 | myosin, heavy polypeptide 9 | 1.76 | |
| NM_031970 | Hspb1 | heat shock 27kDa protein 1 | 1.74 | |
| BG381583 | RGD1565118 * | similar to mKIAA0843 protein | 1.68 | |
| X70706 | Pls3 | plastin 3 (T-isoform) | 1.67 | |
| BM391364 | LOC290704 | 1.60 | 1.67 | |
| BI296011 | Cfl2 * | cofilin 2, muscle | 1.65 | |
| NM_021755 | Lmna | lamin A | 1.63 | |
| NM_130411 | Coro1a | coronin, actin binding protein 1A | 1.63 | |
| BI278813 | Ckap4 * | cytoskeleton-associated protein 4 | 1.60 | |
| BM383953 | LOC367171 | microtubule-associated protein 4 | 1.57 | |
| NM_031675 | Actn4 | actinin alpha 4 | 1.51 | 1.56 |
| AA891834 | Col4a5 * | collagen, type IV, alpha 5 | 1.56 | |
| AI407239 | Myom2 | myomesin 2 | 1.55 | |
| NM_031140 | Vim | vimentin | 1.54 | |
| NM_134452 | Col5a1 | collagen, type V, alpha 1 | 1.52 | |
| AI180161 | Mapre1 | microtubule-associated protein, RP/EB family, member 1 | 1.52 | |
| AW252250 | Nebl * | nebulette | 1.51 | |
| NM_019212 | Acta1 | actin, alpha 1, skeletal muscle | 6.03 | |
| Cell Cycle | ||||
| BG379338 | Rrm2 | ribonucleotide reductase M2 | 6.87 | |
| BE113362 | Cdkn3 * | cyclin-dependent kinase inhibitor 3 | 5.53 | |
| AI409259 | Racgap1 * | Rac GTPase-activating protein 1 | 5.02 | |
| AA944180 | RGD1562047 * | similar to Cyclin-dependent kinases regulatory subunit 2 (CKS-2) | 5.00 | |
| NM_019296 | Cdc2a | cell division cycle 2 homolog A (S. pombe) | 4.40 | |
| AW253821 | Ccnb2 * | cyclin B2 | 3.47 | |
| BI296084 | Ube2c * | ubiquitin-conjugating enzyme E2C | 3.15 | |
| NM_031131 | Tgfb2 | transforming growth factor, beta 2 | 2.06 | 3.06 |
| NM_021989 | Timp2 | tissue inhibitor of metalloproteinase 2 | 1.58 | 2.44 |
| BF417638 | RGD:1359093 | similar to cell division cycle associated 3 | 2.27 | |
| BG380355 | Cdca8 | cell division cycle associated 8 | 2.24 | |
| U05341 | Cdc20 | cell division cycle 20 homolog (S. cerevisiae) | 2.20 | |
| BE117002 | LOC362021 | 2.12 | ||
| AI408269 | Spbc25 | spindle pole body component 25 homolog (S. cerevisiae) | 2.06 | |
| NM_053483 | Kpna2 | karyopherin (importin) alpha 2 | 2.04 | |
| AA874827 | Dlg7 * | discs, large homolog 7 (Drosophila) | 1.84 | |
| AA996882 | Stk6 | serine/threonine kinase 6 | 1.82 | |
| AW920000 | LOC362587 | similar to microfilament and actin filament cross-linker protein isoform b | 1.81 | |
| NM_022381 | Pcna | proliferating cell nuclear antigen | 1.78 | |
| X64589 | Ccnb1 | cyclin B1 | 1.72 | |
| AI407985 | LOC686524 | hypothetical protein LOC686524 | 1.70 | |
| AF140232 | S100a6 | S100 calcium binding protein A6 (calcyclin) | 1.69 | |
| BM386384 | Nap1l1 | nucleosome assembly protein 1-like 1 | 1.65 | |
| NM_053819 | Timp1 | Tissue inhibitor of metalloproteinase 1 | 2.30 | |
| AA957183 | Cit | citron | 1.57 | |
| NM_013174 | Tgfb3 | transforming growth factor, beta 3 | 1.55 | |
| Immunity and Defense | ||||
| AI233530 | C1qtnf3 * | C1q and tumor necrosis factor related protein 3 | 2.67 | |
| BI284441 | Colec12 | collectin sub-family member 12 | 2.59 | |
| BI278802 | Prnp | prion protein | 2.51 | |
| BF389535 | LOC299339 | similar to Tumor necrosis factor, alpha-induced protein 2 (primary response gene B94) | 2.14 | |
| NM_053843 | Fcgr3 | Fc receptor, IgG, low affinity III | 2.10 | |
| AI176519 | Ier3 | immediate early response 3 | 2.08 | |
| L12458 | Lyz | lysozyme | 2.05 | |
| AW918311 | C1qtnf4 * | C1q and tumor necrosis factor related protein 4 | 2.02 | |
| NM_012620 | Serpine1 | serine (or cysteine) proteinase inhibitor, clade E, member 1 | 1.66 | |
| AI228623 | Nptx2 * | neuronal pentraxin II | 1.64 | |
| NM_031971 | Hspa1a | heat shock 70kD protein 1A | 1.54 | |
| Transport (membrane) | ||||
| BI293600 | Slc35b2 | solute carrier family 35, member B2 | 2.08 | 2.64 |
| NM_019354 | Ucp2 | uncoupling protein 2 | 1.50 | |
| Transport (intracellular) | ||||
| NM_022959 | Pamci | peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor | 1.57 | |
| BG381589 | Stx6 | syntaxin 6 | 1.50 | |
| Transport (other) | ||||
| AI170609 | RGD1560252 * | similar to hypothetical protein MGC31967 | 4.02 | 3.10 |
| AI407838 | Ecm1 | extracellular matrix protein 1 | 2.04 | |
| NM_022278 | Glrx1 | glutaredoxin 1 (thioltransferase) | 1.52 | |
| BE111722 | Ndufs2 * | NADH dehydrogenase (ubiquinone) Fe-S protein 2 | 1.52 | |
| Metabolism (lipid) | ||||
| NM_031043 | Gyg1 | glycogenin 1 | 1.59 | 2.64 |
| NM_013200 | Cpt1b | carnitine palmitoyltransferase 1b | 1.60 | 2.43 |
| AF248543 | A3galt2 | alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase) | 1.74 | |
| NM_017235 | Hsd17b7 | hydroxysteroid (17-beta) dehydrogenase 7 | 1.67 | |
| NM_012941 | Cyp51 | cytochrome P450, subfamily 51 | 1.67 | |
| NM_031840 | Fdps | farensyl diphosphate synthase | 1.51 | |
| Metabolism (glycogen) | ||||
| AW919180 | Pygm | muscle glycogen phosphorylase | 1.85 | 1.76 |
| Metabolism (DNA) | ||||
| NM_022674 | H2afz | H2A histone family, member Z | 1.61 | |
| Metabolism (other) | ||||
| AA891760 | RGD1308350 * | similar to hypothetical protein MGC13251 | 1.68 | |
| BG381486 | Large * | like-glycosyltransferase | 1.64 | |
| BM385390 | Uxs1 | UDP-glucuronate decarboxylase 1 | 1.58 | |
| BI282076 | Prdx4 | peroxiredoxin 4 | 1.52 | |
| Protein Modification | ||||
| AI236997 | Dusp14 * | dual specificity phosphatase 14 | 2.24 | |
| NM_130403 | Ppp1r14a | protein phosphatase 1, regulatory (inhibitor) subunit 14A | 1.82 | |
| AW531714 | Ube2t * | ubiquitin-conjugating enzyme E2T (putative) | 1.76 | |
| BI276525 | Ate1 * | arginine-tRNA-protein transferase 1 | 1.70 | |
| BI283703 | Mapkapk2 | MAP kinase-activated protein kinase 2 | 1.69 | |
| AF106659 | Usp2 | ubiquitin specific protease 2 | 1.68 | |
| NM_053323 | Degs | degenerative spermatocyte homolog (Drosophila) | 1.64 | |
| AI010241 | Usp1 * | ubiquitin specific protease 1 | 1.63 | |
| AA799400 | B3galt3 * | UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 | 1.59 | |
| AA849399 | Ctsz | cathepsin Z | 1.54 | |
| BI279788 | Ube2s * | ubiquitin-conjugating enzyme E2S | 1.51 | |
| NM_024135 | Limk2 | LIM motif-containing protein kinase 2 | 1.50 | |
| Protein Folding | ||||
| AI175031 | Dnajb4 * | DnaJ (Hsp40) homolog, subfamily B, member 4 | 1.53 | |
| BG671521 | Hspca | heat shock protein 1, alpha | 1.54 | |
| Signal Transduction | ||||
| NM_019904 | Lgals1 | lectin, galactose binding, soluble 1 | 1.61 | 3.71 |
| NM_012715 | Adm | adrenomedullin | 1.78 | 2.86 |
| BF405151 | Gpr39 * | G protein-coupled receptor 39 | 1.72 | 2.80 |
| NM_053634 | Fcnb | ficolin B | 1.91 | 2.70 |
| NM_033099 | Ptprv | protein tyrosine phosphatase, receptor type, V | 2.27 | |
| BE117002 | RGD1560967 * | similar to Pins | 2.12 | |
| AW253242 | Magi1 * | membrane associated guanylate kinase interacting protein-like 1 | 1.74 | |
| X78595 | Npr3 | natriuretic peptide receptor 3 | 1.74 | |
| BG378926 | S100a11 | S100 calcium binding protein A11 (calizzarin) | 1.73 | |
| BI276015 | RGD1559882 * | similar to hypothetical protein E130310N06 | 1.66 | |
| BM386204 | Ran | RAN, member RAS oncogene family | 1.65 | |
| BI295991 | Rab2l | RAB2, member RAS oncogene family-like | 1.60 | |
| NM_022236 | Pde10a | phosphodiesterase 10A | 1.56 | 1.56 |
| NM_012823 | Anxa3 | annexin A3 | 1.51 | |
| NM_053299 | Ubd | ubiquitin D | 1.72 | |
| M35297 | Mrgprf | MAS-related GPR, member F | 1.79 | |
| Transcription | ||||
| BM385445 | Top2a | topoisomerase (DNA) 2 alpha | 3.37 | |
| L81174 | Ankrd1 | ankyrin repeat domain 1 (cardiac muscle) | 2.62 | 3.02 |
| NM_031628 | Nr4a3 | nuclear receptor subfamily 4, group A, member 3 | 2.34 | |
| NM_017187 | Hmgb2 | high mobility group box 2 | 2.04 | |
| NM_131902 | Cdkn2c | cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) | 2.01 | |
| NM_017365 | Pdlim1 | PDZ and LIM domain 1 (elfin) | 2.00 | |
| AI170362 | Nfkb2 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 2, p49/p100 | 1.95 | |
| U17565 | Mcmd6 | mini chromosome maintenance deficient 6 (S. cerevisiae) | 1.88 | |
| NM_053583 | Zfp423 | zinc finger protein 423 | 1.87 | |
| BM387864 | Lrrfip1 | similar to FLI-LRR associated protein-1 | 1.76 | |
| BG664147 | Ptrf * | polymerase I and transcript release factor | 1.65 | |
| BG380385 | Srf * | serum response factor | 1.95 | 1.64 |
| BF403027 | Hdac5 | histone deacetylase 5 | 1.64 | |
| AI179264 | Creb3 | cAMP responsive element binding protein 3 | 1.50 | |
| Homeostasis | ||||
| BI285437 | Nxn * | nucleoredoxin | 1.62 | |
| Nucleus | ||||
| BE104102 | RGD1306774 * | similar to SPT3-associated factor 42 | 1.83 | |
| Membrane | ||||
| BM385031 | Plp2 | proteolipid protein 2 | 1.76 | 2.55 |
| BM388441 | RGD1311946 * | similar to RIKEN cDNA 1810055G02 | 1.97 | |
| NM_030847 | Emp3 | epithelial membrane protein 3 | 1.89 | |
| AW917760 | RGD1564216 * | similar to Myoferlin (Fer-1 like protein 3) | 1.88 | |
| AI009530 | MGC72614 | hypothetical LOC310540 | 1.86 | |
| BI296048 | Myadm | myeloid-associated differentiation marker | 1.55 | 1.77 |
| J03867 | Dia1 | diaphorase 1 | 1.60 | |
| BM385463 | Tmem43 | transmembrane protein 43 | 1.55 | |
| AI230273 | RGD:735199 | Unknown (protein for MGC:72987) | 1.55 | |
| BF283798 | Nipsnap3a | nipsnap homolog 3A (C. elegans) | 1.53 | |
| AA850909 | Pvrl2 * | poliovirus receptor-related 2 (herpesvirus entry mediator B) | 1.50 | |
| BI290029 | RGD1562920 * | similar to Aig1 protein | 1.50 | |
| AI407016 | RGD1307736 * | similar to Hypothetical protein KIAA0152 | 1.55 | |
| BI294974 | Ldlr | low density lipoprotein receptor | 1.69 | |
| Developmental Processes | ||||
| NM_031549 | Tagln | transgelin | 69.77 | 38.66 |
| NM_012636 | Pthlh | parathyroid hormone-like peptide | 3.13 | |
| NM_030584 | Sost | sclerostin | 3.12 | |
| AW141680 | Bmp6 | bone morphogenetic protein 6 | 2.36 | |
| NM_019242 | Ifrd1 | interferon-related developmental regulator 1 | 2.05 | 2.32 |
| AW251450 | Mustn1 | musculoskeletal, embryonic nuclear protein 1 | 2.13 | |
| AI235465 | Ssg1 | steroid sensitive gene 1 | 2.07 | |
| AW435036 | Smtn * | smoothelin | 1.65 | |
| BI290551 | Fnbp1 | Formin binding protein 1 | 1.60 | |
| BI275485 | Sema3b * | semaphorin 3B, immunoglobulin domain, secreted | 1.57 | |
| AW144216 | Enpep | glutamyl aminopeptidase | 2.11 | 1.57 |
| BG666787 | Gmfg | glia maturation factor, gamma | 1.56 | |
| BM384088 | Socs2 | suppressor of cytokine signaling 2 | 1.54 | |
| NM_031114 | S100a10 | S100 calcium binding protein A10 (calpactin) | 1.51 | |
| Others | ||||
| AI229404 | RGD1566097 * | similar to Anillin | 2.47 | 8.41 |
| BI295828 | 2.28 | 3.31 | ||
| BI279587 | 2.12 | 3.01 | ||
| BI283695 | 1.73 | 2.48 | ||
| AW531909 | 2.44 | |||
| BF419834 | 1.62 | 2.29 | ||
| BF415061 | RGD1307034 * | similar to hypothetical protein CG003 | 2.21 | |
| BF408518 | RGD1305081 * | similar to ionized calcium binding adapter molecule 2 (Iba2) | 1.98 | 2.16 |
| AI712694 | RGD1308747 * | similar to hypothetical protein FLJ10156 | 2.15 | |
| BI296728 | RGD1564957 * | similar to RIKEN cDNA 3110007P09 | 2.04 | |
| AI176172 | 2.03 | |||
| BM387112 | 1.71 | 2.03 | ||
| AI071000 | 2.00 | |||
| AA799328 | RGD1560913 * | similar to expressed sequence AW413625 | 1.93 | |
| BE096535 | transcribed locus, strongly similar to XP_574462.1 similar to hypoth. protein C230069C04 | 1.89 | ||
| BG378155 | RGD1565079 * | similar to hypothetical protein MGC17839 | 1.88 | |
| AA943808 | RGD1307215 | similar to protein phosphatase 1, inhibitory subunit 1C; thymocyte ARPP | 1.82 | |
| AW143197 | 1.79 | |||
| AW529960 | 1.78 | |||
| AI177743 | LOC498261 | 1.72 | ||
| AI317841 | Gramd3 | GRAM domain containing 3 | 1.69 | |
| BI303106 | 1.64 | |||
| BF561368 | RGD1306959 * | similar to C11orf17 protein | 1.63 | |
| AW253004 | CDNA clone IMAGE:7317367 | 1.62 | ||
| BF398756 | 1.62 | |||
| AI009167 | Zfp451 * | zinc finger protein 451 | 1.62 | |
| AI412389 | 1.61 | |||
| BE111057 | 1.60 | |||
| BI282694 | RGD1565037 * | similar to selenoprotein SelM | 1.60 | |
| AI231225 | 1.58 | |||
| AA942716 | Hn1 | hematological and neurological expressed sequence 1 | 1.56 | |
| BF284519 | 1.55 | |||
| BG671786 | 1.53 | |||
| AW914928 | 1.53 | |||
| AI113146 | Acpl2 | acid phosphatase-like 2 | 1.51 | |
| AI170820 | RGD1310383 * | similar to T-cell activation protein phosphatase 2C | 1.50 | |
| AA800892 | RGD1563599 * | similar to putative SH3BGR protein | 1.81 | |
| BG380430 | RGD1564105 * | similar to RIKEN cDNA B130052G07 | 1.54 | |
| NM_021584 | Ania4 | activity and neurotransmitter-induced early gene protein 4 (ania-4) | 2.53 | |
| AA997359 | Serpinb6 | serine (or cysteine) peptidase inhibitor, clade B, member 6 | 1.54 | |
| NM_012618 | S100a4 | S100 calcium-binding protein A4 | 1.80 | |
| NM_022382 | Pde4dip | phosphodiesterase 4D interacting protein (myomegalin) | 1.70 | |
| AI112962 | Rcn * | reticulocalbin | 1.92 | |
| AI232065 | Arhgap18 * | Rho GTPase activating protein 18 | 1.55 | |
List of 234 differentially regulated genes (>1.5 fold) in PHN induced rats on day three and or day six. Genes are annotated with NCBI Gene Symbols and grouped according to biological function. Starred (*) Gene Symbols mark predicted genes.