Table 1.
Cellular transcripts showing over two fold alterations following IBV infection in ovo
| Accession number | Gene name | Fold change in transcription (standard deviation) PI |
|||
|---|---|---|---|---|---|
| 6 h | 24 h | 48 h | 72 h | ||
| Kinases and phosphatases genes | |||||
| SWP:143Z_HUMAN | kcip-1, factor activating exoenzyme s, fas | 69.76 (41.6) | 26.43 (18.1) | 20.11 (13.7) | 22.02 (11.0) |
| Gb AA23736.1 | Protein kinase [homo sapiens] >gi|7513329|pir | 6.13 (3.05) | 2.53 (0.76) | 1.08 (0.42) | 1.01 (0.34) |
| Ref NP_O67085.1 | Acid phosphatase 1, soluble [rattus norvegicus] | 1.28 (0.38) | 4.58 (0.42) | 1.26 (0.30) | 1.04 (0.17) |
| EMB:CAA83657 | Protein-tyrosine-phosphatase alpha [gallus gallu] | 10.61 (1.62) | 11.76 (0.19) | 4.08 (0.59) | 0.96 (0.18) |
| Inteferon induced genes | |||||
| SWP:INI2_PANTR | Interferon-induced protein 6–16 precursor | 0.85 (0.02) | 3.86 (0.55) | 1.16 (0.01) | 1.12 (0.53) |
| EMB:Q9QXH3 | Alpha-interferon inducible protein (fragment) p27-h | 0.86 (0.02) | 3.22 (1.51) | 1.48 (1.32) | 1.52 (0.66) |
| EMB:AAH02704 | Similar to signal transducer and activator of transcription 1 | 1.77 (1.09) | 1.11 (0.28) | 0.64(0.23) | 1.16 (0.27) |
| WP:STA1_HUMAN | Signal transducer and activator of transcription 1-alpha/beta | 3.03 (0.2) | 1.45 (0.14) | 3.01 (1.07) | 0.96 (0.31) |
| SWP:IFT1_HUMAN | Interferon-induced protein with tetratricopep | 21.94 (7.2) | 35.27 (2.28) | 13.98 (2.18) | 0.99 (0.14) |
| Gb AAH44176.1 | Similar to G protein beta subunit-like [danio rerio] | 17.43 (3.34) | 1.12 (0.59) | 1.07 (0.72) | 1.30 (0.32) |
| Chemoatttractant and adhesion molecules | |||||
| SWP:EMF1_CHICK | Embryo fibroblast protein 1 precursor (emf-1, 9e3, cef4, human il-8 homolog) | 1.21 (0.56) | 4.87 (2.95) | 1.03 (0.20) | 1.19 (0.31) |
| SWP:LSP1_MOUSE | Lymphocyte specific protein-1 | 61.31 (29.35) | 22.84 (13.7) | 4.43 (1.7) | 1.25 (0.64) |
| Signal transduction | |||||
| Gb AAH05446.1 | Adenylyl cyclase-associated cap protein homolog 1 | 1.04 (0.09) | 1.00 (0.05) | 0.46 (0.03) | 0.91 (0.03) |
| Transcription regulation | |||||
| SWP:TYY1_HUMN | Transcriptional repressor protein yy1 | 1.89 (1.2) | 7.21 (1.9) | 0.83 (0.6) | 1.07 (0.3) |
| Gb AAH19668.1 | taf12 rna polymerase ii, tata box binding protein … | 0.78 (0.2) | 7.90 (0.86) | 1.03 (0.06) | 1.32 (0.82) |
| SWP:PTB_PIG | q29099 polypyrimidine tract-binding protein (ptb) (hnrnp1) | 0.82 (0.12) | 8.78 (3.82) | 1.26 (0.28) | 1.03 (0.21) |
| Ref XP_128452.2 | Similar to enhancer factor i chain a-d-rat [m] … | 1.86 (0.75) | 0.63 (0.3) | 3.03 (1.3) | 1.33 (0.74) |
| EMB:CAB62917.1 | E1a binding protein p300 ∼ match: proteins: sw:q09 … | 2.22 (1.3) | 0.51 (0.2) | 1.35 (0.72) | 1.27 (0.21) |
| Gb AAD04629.1 | Pcaf-associated factor 400 [homo sapiens] | 0.43 (0.16) | 0.87 (0.34) | 24.29 (11.2) | 0.93 (0.11) |
| Atigen presentation | |||||
| EMB:O42404 | cd80-like protein precursor. | 0.74 (0.23) | 2.77 (0.40) | 0.96 (0.09) | 0.97 (0.33) |
| Vesicular protein trafficking and ubiqutin proteasome | |||||
| Ref NP_O58040.1| | Clathrin, light polypeptide (lca) [mus musculus… | 3.24 (0.21) | 6.36 (0.44) | 2.92 (1.8) | 1.04 (0.4) |
| SWP:SR54_HUMAN | Signal recognition particle 54 kda protein (s) | 1.32 (0.46) | 6.07 (2.24) | 1.22 (0.65) | 1.01 (0.32) |
| SWP:TERA_HUMAN | p55072 transitional endoplasmic reticulum atpase | 2.20 (0.15) | 1.10 (0.66) | 1.68 (0.86) | 1.08 (0.25) |
| EMB:Q9Y4Z6 | Vacuolar protein sorting. | 1.43 (0.50) | 2.00 (0.56) | 0.47 (0.31) | 1.01 (0.43) |
| Ref NP_003560.1 | Syntaxin 7 [homo sapiens] >gi|2337920|gb|aac518 … | 1.42 (0.08) | 0.46 (0.39) | 0.68 (0.59) | 1.06 (0.19) |
| Gb AAH38447.1 | Similar to coatomer protein complex, subunit alph … | 1.01 (0.08) | 0.93 (0.13) | 1.02 (0.12) | 8.47 (4.23) |
| SWP:RTC0_HUMAN | GTP-binding protein tc10. | 0.16 (0.07) | – | 2.4 (0.4) | 1.00 (0.20) |
| Ref XP_214136.1 | Similar to 26s proteasome non-atpase regulatory … | 2.11 (0.75) | 1.12 (0.78) | 19.87 (2.78) | 0.96 (0.19) |
| SWP:UBPI_HUMAN | Ubiquitin carboxyl terminal hydrolase 18 (Ubp) | 34.74 (10.8) | 21.70 (3.52) | 0.929 (0.14) | 0.890 (0.23) |
| SWP:FUCO_HUMAN | Tissue alpha-1-fucosidase precursor | 1.01 (0.56) | 4.63 (0.77) | 2.46 (0.72) | 0.72 (0.30) |
| Translation | |||||
| SWP:EF1A_CHICK | Elongation factor 1-alpha-1 | 2.24 (0.26) | 1.09 (0.27) | 2.03 (0.76) | 0.94 (0.13) |
| Gb AAO40745.1 | Eukaryotic elongation factor 1-alpha [canis family. | 0.79 (0.31) | 1.53 (0.42) | 4.14 (2.1) | 1.04 (0.01) |
| Gb AAD16874.1 | Peptide elongation factor-1 beta [gallus gallus] | 1.11 (0.58) | 0.93 (0.50) | 0.33 (0.07) | 0.94 (0.18) |
| SWP:IF42_HUMAN | Eukaryotic initiation factor 4a-ii (eif-4a-ii) | 0.83 (0.28) | 7.18 (1.24) | 1.05 (0.30) | 1.13 (0.64) |
| SWP:RL3_BOVIN | 60s ribosomal protein l3. | 3.90 (0.7) | 0.48 (0.65) | 1.09 (0.33) | 1.13 (0.46) |
| Ref XP_110140.2 | Eukaryotic translation initiation factor 3, sub… | 0.34 (0.21) | 0.64 (0.10) | 1.15 (0.17) | 1.26 (0.27) |
| EMB:CAA57493.1 | Ribosomal protein s6 [gallus gallus] >gi|1085253. | 5.04 (1.6) | 0.61 (0.14) | 4.04 (1.6) | 0.75 (0.45) |
| EMB:CAA44568.1 | Ribosomal protein homologous to yeast s24 [homo … | 0.33 (0.10) | 3.60 (1.66) | 1.63 (0.2) | 1.15 (0.47) |
| Ref NP_001347.2 | Dead/h (asp-glu-ala-asp/his) box polypeptide 3;(DDX3) … | 0.80 (0.3) | 3.30 (0.88) | 1.00 (0.15) | 0.93 (0.5) |
| Mitochondrial protein | |||||
| Dbj BAC57503 | Cytochrome oxidase subunit ii | 0.64 (0.28) | 2.97 (1.2) | 0.69 (0.40) | 0.96 (0.40) |
| Dbj BAC57502.1 | Cytochrome oxidase subunit I [coturnix chinensis] | 2.07 (0.60) | 1.15 (0.40) | 1.14 (0.1) | 2.75 (0.96) |
| Ref NP_620316.1 | Cytochrome oxidase subunit I | 1.25 (0.10) | 1.89 (1.2) | 0.11 (0.08) | 0.97 (0.27) |
| Cell cycle | |||||
| Ref XP_220119.1 | Similar to G2/mitotic specific cyclin b | 0.84 (0.28) | 1.09 (0.5) | 3.29 (1.02) | 1.06 (0.17) |
| SWP:CGA2_CHICK | Cyclin a2 | 0.84 (0.22) | 0.31 (0.29) | 4.10 (0.95) | 0.96 (0.60) |
| SWP:CCT2_HUMAN | o60583 cyclin t2 | 1.25 (0.94) | 0.99 (0.20) | 0.94 (0.20) | 4.88 (1.02) |
| Cell physiology and development | |||||
| SWP:FKBB_HUMAN | 12.6 kDa fk 506 binding protein | 1.25 (0.57) | 0.91 (0.76) | 0.29 (0.19) | 0.99 (0.13) |
| Gb AAN28379.1 | ABl-interactor 1 [homo sapiens] | 16.61 (7.2) | 0.91 (0.21) | 1.08 (0.11) | 1.42 (0.42) |
| Cytoskeleton and motor proteins | |||||
| SWP:ACT2_HALRO | p27130 actin, muscle 2/4/4a. | 0.12 (0.07) | 1.52 (1.17) | 1.80 (1.7) | 1.19 (0.73) |
| PIR:S06117 | S06117 myosin heavy chain, nonmuscle | 1.23 (0.19) | 3.10 (1.63) | 0.61 (0.22) | 0.79 (0.23) |
| Ref NP_003184.1 | β-Tubulin cofactor e [homo sapiens] >gi|1425.. | 4.81 (1.73) | 1.39 (0.52) | 1.03 (0.19) | 2.16 (1.03) |
| Gb AAK27259.1 | β-Actin [ambystoma mexicanum] | 1.69 (0.58) | 5.71 (2.19) | 0.96 (0.22) | 0.95 (0.06) |
| EMB:Q23882 | Slime mold (d.discoideum) actin mrna itl-1, 3 | 0.81 (0.37) | 0.96 (0.13) | 1.03 (0.15) | 2.22 (0.77) |
| Extracellular matrix proteins | |||||
| SWP:CA11_CHICK | Collagen alpha 1(i) chain precursor. | 0.85 (0.28) | 1.20 (0.33) | 2.17 (0.49) | 0.88 (0.16) |
| SWP:HAS2_CHICK | Hyaluronan synthase 2 | 1.07 (0.12) | 2.59 (0.07) | 0.51 (0.03) | 0.98 (0.18) |
| EMB:O00199 | Integral membrane serine protease seprase | 10.23 (2.6) | 0.83 (0.49) | 0.77 (0.30) | 0.96 (0.13) |
| EMB:Q91002 | Thrombospondin-4 (fragment) | 1.79 (0.47) | 6.88 (3.50) | 1.62 (0.90) | 0.68 (0.06) |
| SWP:PEDF_MOUSE | Pigment epithelium-derived factor precursor | 1.81 (0.52) | 2.57 (0.94) | 2.38 (0.74) | 1.21 (0.27) |
| SWP:ITB1_CHICK | Integrin beta-1 precursor (csat antigen) (jg2) | 0.08 (0.11) | 0.99 (0.02) | 0.15 (0.10) | 5.49 (1.47) |
| SWP:PEDF_BOVIN | Pigment epithelium-derived factor precursor | 0.90 (0.3) | 0.81 (0.22) | 2.56 (1.03) | 1.32 (0.7) |
| Tumor associated proteins | |||||
| EMB:Q9JLL0 | Cysteine-rich repeat-containing protein crim1 | 0.74 | 8.21 (2.30) | 19.33 (9.57) | 1.33 (0.84) |
| Hypothetical proteins | |||||
| EMB:Q9H0P6 | Hypothetical 38.9 kDa protein. | 7.02 (2.53) | 1.51 (0.38) | 1.32 (0.13) | 0.82 (0.26) |
| EMB:Q9Y3V7 | Hypothetical 63.3 kDa protein (fragment) | 1.67 (0.01) | 2.46 (0.94) | 0.925 (0.66) | 0.985 (0.07) |
| EMB:Q9H0I1 | Hypothetical 83.8 kDa protein. | 2.45 (1.12) | 1.21 (0.20) | 1.318 (0.28) | 1.101 (0.23) |
| EMB:CAD38974.1 | Hypothetical protein [homo sapiens] | 0.21 (0.09) | 1.30 (0.04) | 10.977 (4.15) | 0.801 (0.12) |
| Gb AAA27977.1 | Hypothetical protein c50c3.6 [caenorhabditis eleg …] | 1.25 (0.61) | 0.99 (0.96) | 8.675 (2.53) | 1.037 (0.23) |
| Ref XP_043624.2 | Similar to hypothetical protein dkfzp434e1822.1 … | 1.76 (0.26) | 2.11 (1.09) | 1.067 (0.59) | 1.056 (0.42) |
| EMB:CAB43259.1 | Hypothetical protein [homo sapiens] | 4.12 (2.01) | 0.72 (0.36) | 0.956 (0.87) | 0.971 (0.16) |
| Metabolism | |||||
| EMB:AAB34334 | Protein phosphatase 1 gamma 1 (fragment) | 1.56 (0.77) | 0.49 (0.34) | 0.744 | 0.939 (0.56) |
| EMB:AAD02474 | Glyceraldehyde-3-phosphate dehydrogenas | 0.99 (0.51) | 1.85 (0.85) | 4.67 (2.24) | 0.86 (0.60) |
| SWP:SYI_HUMAN | Isoleucyl-trna synthetase, cytoplasmic (ec 6) | 0.94 (0.15) | 0.88 (0.10) | 0.38 (0.14) | 1.69 (0.28) |
| SWP:ATP6_CHICK | Atp synthase a chain (ec 3.6.1.34) (protein 6) | 1.58 (0.38) | 2.29 (0.86) | 0.95 (0.07) | 1.13 (0.21) |
| Gb AAB24816.1 | Farnesyltransferase alpha subunit [human, peptide …] | 2.24 (0.85) | 1.08 (0.92) | 1.01 (0.28) | 0.95 (0.30) |
| SWP:ENOA_CHICK | Alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) | 7.71 (2.44) | 0.68 (0.33) | 1.27 (0.52) | 0.67 (0.17) |
| SWP:PNAD_PIG | Protein n-terminal asparagine amidohydrolase | 3.83 (1.61) | 0.79 (0.3) | 0.92 (0.06) | 1.06 (0.41) |
| SWP:PWP2_HUMAN | Periodic tryptophan protein 2 homolog (pwp2) | 0.39 (0.18) | 1.40 (1.03) | 0.67 (0.33) | 4.46 (1.73) |
| Gb AAC98906.1 | Chaperonin-containing tcp-1 beta subunit homolog … | 0.72 (0.24) | 0.54 (0.33) | 0.73 (0.43) | 0.96 (0.30) |
| Pdb 1AK6 | Destrin, nmr, minimized average structure >gi|2624765 … | 1.20 (0.39) | 0.81 (0.18) | 2.34 (0.50) | 1.07 (0.52) |
| Ref NP_067085.1 | Acid phosphatase 1, soluble [rattus norvegicus] … | 1.28 (0.38) | 4.58 (1.42) | 1.26 (0.30) | 1.04 (0.17) |
| Gb AAA40873.1 | Carboxypeptidase e (ec 3.4.17.10) | 2.59 (0.62) | 1.18 (0.58) | 1.11 (0.53) | 0.93 (0.28) |
| Gb AAA66286.1 | Ornithine decarboxylase | 1.29 (0.57) | 1.50 (0.81) | 10.62 (3.44) | 0.85 (0.46) |
| Nucleic acid binding | |||||
| SWP:N6M1_HUMAN | Putative n6-dna-methyltransferase | 0.57 (0.25) | 0.73 (0.26) | 0.32 | 1.20 (0.34) |
| Unknown function | |||||
| EMB:AAH06414 | Similar to kiaa0952 protein (fragment) | 1.02 (0.03) | 1.21 (0.45) | 9.93 (2.58) | 1.02 (0.47) |
| EMB:Q9D0E4 | 2610021k23rik protein. | 2.59 (0.96) | 1.35 (0.48) | 0.93 (0.58) | 0.92 (0.30) |
| EMB:Q9H7T5 | cdna flj14273 fis, clone place1004913 (fragme | 3.54 (1.03) | 1.49 (0.46) | 1.34 (0.47) | 1.05 (0.45) |
| EMB:Q9NUM1 | cdna flj11277 fis, clone place1009404 | 1.40 (0.59) | 2.58 (0.70) | 1.00 (0.65) | 1.84 (0.86) |
| EMB:Q9ULD7 | kiaa1283 protein (fragment). | 1.24 (0.08) | 2.99 (0.83) | – | 1.03 (0.27) |
| EMB:AAH02380 | Inknown (protein for image:2961244) (fr) | 4.20 (0.56) | 1.01 (0.44) | 2.78 (0.41) | 1.08 (0.46) |
| EMB:Q9H3F0 | mstp034 | 2.21 (1.03) | 1.43 (0.32) | 11.076 (4.56) | 1.11 0.30) |
| EMB:Q9D0V1 | 1110067l12rik protein | 1.10 (0.45) | 2.28 (1.06) | 0.66 (0.37) | 1.16 (0.41) |
| GEN:CAC22485 | Unnamed protein product [homo sapiens] | 5.43 (1.26) | 1.11 (1.04) | 0.37 | 0.96 (0.11) |
| EMB:Q9D9D0 | 1700101g24rik protein | 0.98 (0.36) | 2.36 (1.11) | 0.73 (0.15) | 1.22 (0.23) |
| Dbj BAB30848.1 | Unnamed protein product [mus musculus] | 0.93 (0.43) | 0.83 (0.43) | 4.92 (1.94) | 1.09 (0.15) |
| Dbj BAB28442.1 | Unnamed protein product [mus musculus] >gi|23396 … | 14.17 (6.30) | 6.05 (2.10) | 10.01 (3.63) | 0.88 (0.35) |
| EMB:Q9D8V0 | 1200006o09rik protein | 0.98 (0.54) | 17.24 (5.62) | 0.73 (0.44) | 1.02 (0.44) |
| EMB:Q9H8I2 | CDNA FLJ14005 fis, clone Y79AA1002361 | 1.72 (0.69) | 1.19 (0.78) | – | 0.48 (0.05) |
| Dbj BAC29089.1 | Unnamed protein product [mus musculus] | 6.88 (2.38) | 1.30 (0.90) | 1.08 (0.48) | 0.96 (0.25) |
| Ref XP_032996.1 | Similar to kiaa0819 protein [homo sapiens] | 1.00 (0.75) | 0.47 (0.30) | 1.37 (1.06) | 1.20 (0.48) |
| Dbj BAA07556.1 | kiaa0074∼the ha1438 gene product is related to a … | 16.52 (4.38) | 1.31 (0.77) | 0.70 (0.39) | 1.06 (0.12) |
| Dbj BAA05837.1 | kiaa0045 [homo sapiens] >gi|10863903|ref|np_0042 … | 1.75 (0.38) | 1.66 (0.22) | 4.22 (2.04) | 1.15 (0.26) |
| Ref NP_058040.1 | Clathrin, light polypeptide (lca) [mus musculus …] | 2.64 (0.21) | 1.20 (0.21) | 1.60 (0.23) | 1.04 (0.41) |
| Ref XP_216872.1 | Similar to riken cdna 2410003l22 [mus musculus] … | 36.14 (8.97) | 1.31 (0.77) | 28.83 (6.00) | 1.00 (0.28) |
| Ref XP_214380.1 | Similar to riken cdna 4933405k01 [mus musculus] … | 4.05 (1.31) | 0.92 (0.30) | 1.10 (0.42) | 1.03 (0.30) |
| Dbj BAB28379.1 | Unnamed protein product [mus musculus] | 2.24 (0.33) | 1.13 (0.43) | 0.65 (0.48) | 1.38 (0.58) |
| Ref NP_056371.1 | kiaa0440 protein [homo sapiens] >gi|4151330|gb … | 1.20 (1.03) | 1.67 (0.60) | 10.95 (3.08) | 1.11 (0.40) |
| Dbj BAA91948.1 | Unnamed protein product [homo sapiens] >gi|89228 … | 21.66 (8.86) | 1.08 (0.85) | 1.00 (0.43) | 0.90 (0.20) |
| Dbj BAB14688.1 | Unnamed protein product [homo sapiens] | 2.67 (0.83) | 1.02 (0.59) | 0.93 (0.13) | |
| Dbj BAB26968.1 | Unnamed protein product [mus musculus] >gi|21312 … | 0.70 (0.46) | 0.91 (0.51) | 13.77 (6.58) | 0.900 (0.17) |
| Dbj BAB15047.1 | Unnamed protein product [homo sapiens] | 1.09 (0.43) | 4.48 (2.06) | 0.87 (0.32) | 1.11 (0.21) |
| Ref XP_225174.1 | Similar to riken cdna 4833439l19; expressed seq … | 2.11 (0.26) | 1.16 (0.35) | 0.94 (0.25) | 0.91 (0.39) |
| Dbj BAC11615.1 | Unnamed protein product [homo sapiens] | 24.36 (9.28) | 1.22 (1.27) | 1.40 (0.94) | 0.95 (0.23) |
| Dbj BAC36160.1 | Unnamed protein product [mus musculus] | 1.23 (0.13) | 1.30 (0.29) | 5.48 (2.42) | 1.24 (0.34) |
| Dbj BAC36765.1 | Unnamed protein product [mus musculus] | 1.01 (0.46) | 1.18 (0.22) | 1.10 (0.45) | 5.01 (2.41) |
| Dbj BAC29089.1 | Unnamed protein product [mus musculus] | 6.88 (3.38) | 1.30 (0.90) | 1.08 (0.49) | 0.96 (0.25) |
| Transport protein | |||||
| SWP:NTCH_RAT, P28570 | Sodium-dependent choline transporter (chot1). | 1.75 (0.70) | 2.32 (1.00) | 1.11 (0.82) | 1.06 (0.21) |
| SWP:ABF2_HUMAN | Iron inhibited abc transporter 2; abcf2 | 48.19 (20.75) | 22.79 (8.78) | 15.94 (6.32) | 19.82 (8.47) |
| RNA regulation | |||||
| SWP:RSFR_CHICK | p30374 ribonuclease homolog precursor (rsfr) | 1.54 (0.13) | 5.87 (1.75) | 5.96 (1.66) | 1.93 (1.13) |