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Table 3 Annotation of cell cycle genes by cluster

From: Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

FB cluster
EST Genbank acc. Best A. thaliana hita e value Descriptionb
5019 CN936403 AT5G44680.1 1e-40 methyladenine glycosylase family protein
5126 EB107042 AT2G38620.1 9e-80 CDKB1;2 cell division control protein
33679 CN929052 AT2G47420.1 9e-18 dimethyladenosine transferase
59120 CN862228 AT5G42320.1 2e-12 zinc carboxypeptidase family protein
67405 CN864463 AT5G53000.1 3e-31 protein phosphatase 2A-associated 46 kDa protein
86932 EB119954 AT1G01490.1 2e-19 heavy-metal-associated domain-containing protein
124169 CN937737 AT1G18660.1 3e-67 zinc finger (C3HC4-type RING finger) family protein
134415 CN888558 AT3G62600.1 1e-153 DNAJ heat shock family protein
140667 CN938500 AT2G24490.1 8e-46 replication protein, putative
222173 CN876164 AT4G11010.1 9e-47 nucleoside diphosphate kinase 3, mitochondrial (NDK3)
226032 EG631233 AT3G08500.1 3e-48 myb family transcription factor (MYB83)
254247 CN912925 AT1G10290.1 3e-49 dynamin-like protein 6 (ADL6)
256645 EB151655 AT1G79350.1 1e-77 EMB1135 DNA-binding protein, putative
257305 CN908171 AT3G57550.1 3e-41 guanylate kinase 2 (GK-2)
258270 CN914773 AT2G30110.1 1e-179 ubiquitin activating enzyme 1 (UBA1)
264677 CN910366 AT3G48160.2 6e-68 E2F-like repressor E2L3 (E2L3)
264992 CN917058 AT5G23430.1 1e-53 transducin family protein/WD-40 repeat family protein
EFD cluster
EST Genbank acc. Best A. thaliana hit e value Description
12163 EB109178 AT3G28030.1 2e-27 UV hypersensitive protein (UVH3)
14094 CN931474 AT2G01440.1 6e-15 ATP-dependent DNA helicase, putative
15274 CN932236 AT3G25500.1 8e-26 FH2 domain-containing protein
19893 CN925129 AT1G73540.1 3e-11 ATNUDT21 MutT/nudix family protein
29516 EB111254 AT2G39730.1 9e-72 RuBisCO activase
31066 CN927871 AT3G23890.1 8e-13 DNA topoisomerase II
33027 CN928590 AT3G25500.1 3e-39 FH2 domain-containing protein
43417 EB113579 AT1G69770.1 3e-06 chromomethylase 3 (CMT3)
45185 CN857495 AT5G05510.1 2e-25 low similarity to SP:O60566 Mitotic checkpoint serine/threonine-protein kinase BUB1 β
62518 EB116342 AT3G08910.1 7e-67 DNAJ heat shock protein
64262 CN850169 AT2G30200.1 1e-148 T27E13_6
85474 CN869267 AT1G68760.1 6e-54 ATNUDT1 MutT/nudix family protein
91885 CN871666 AT1G10520.1 3e-15 DNA polymerase lambda (POLL)
93419 CN874495 AT5G26751.1 4e-58 shaggy-related protein kinase α/ASK-α (ASK1)
95093 CN875141 AT5G18110.1 5e-60 novel cap-binding protein (nCBP)
105540 CN886787 AT3G51770.1 1e-111 similar to tetratricopeptide repeat (TPR)-containing protein
111728 EB124553 AT1G44900.1 3e-50 DNA replication licensing factor
118006 EB125634 AT2G21790.1 8e-45 ribonucleoside-diphosphate reductase small chain, putative
119405 CN887179 AT1G68010.1 1e-81 glycerate dehydrogenase/NADH-dependent hydroxypyruvate reductase
120390 CN890521 AT1G21660.1 7e-12 low similarity to SP:O14976 Cyclin G-associated kinase
138266 CN937814 AT2G17120.1 3e-79 peptidoglycan-binding LysM domain-containing protein
142020 CN939277 AT2G38810.1 2e-48 histone H2A, putative
142920 EB127800 AT5G57850.1 2e-08 aminotransferase class IV family protein
148629 EB138792 AT3G22630.1 2e-36 20S proteasome β subunit D (PBD1) (PRGB)
149453 CN897394 AT5G55230.1 1e-118 ATMAP65-1 Binds and bundles microtubules
149668 CN897544 AT4G36080.1 1e-103 FAT domain-containing protein/phosphatidylinositol 3- and 4-kinase family protein
151134 EB139596 AT2G42580.1 5e-24 tetratricopeptide repeat (TPR)-containing protein
151602 CN898773 AT5G13780.1 8e-81 GCN5-related N-acetyltransferase, putative, similar to ARD1 subunit
152213 CN940414 AT2G35040.1 1e-112 AICARFT/IMPCHase bienzyme family protein
153604 EB140203 AT1G55350.1 0 EMB1275 calpain-type cysteine protease family
153992 CN900578 AT2G21790.1 1e-160 R1 ribonucleoside-diphosphate reductase small chain, putative
155385 CN901052 AT2G21790.1 2e-83 R1 ribonucleoside-diphosphate reductase small chain, putative
155966 CN901211 AT5G61060.1 2e-34 histone deacetylase family protein
159200 CN940759 AT2G14880.1 6e-36 SWIB complex BAF60b domain-containing protein
162529 CN942994 AT3G44110.1 1e-152 DNAJ heat shock protein, putative (J3)
163128 CN943384 AT1G20930.1 1e-102 CDKB2;2 cell division control protein, putative
163154 CN943405 AT5G61060.1 2e-84 histone deacetylase family protein
166835 EE663942 AT3G17880.1 1e-58 tetratricoredoxin (TDX)
170408 EB140959 AT3G08910.1 7e-59 DNAJ heat shock protein, putative
170963 CN882668 AT2G46225.1 2e-20 ABI1L1 Encodes a subunit of the WAVE complex
171493 CN883039 AT2G29570.1 1e-111 PCNA2 proliferating cell nuclear antigen 2 (PCNA2)
172325 CN883596 AT5G08020.1 7e-91 similar to replication protein A1 (Oryza sativa)
173799 EB141951 AT2G27960.1 6e-37 CKS1 cyclin-dependent kinase
180731 CN904791 AT1G75690.1 2e-55 chaperone protein dnaJ-related
181072 CN904980 AT3G18190.1 0 chaperonin, putative
184975 EB148197 AT5G44680.1 1e-90 methyladenine glycosylase family protein
186444 EB149644 AT3G19420.1 2e-12 MLD14.22
186960 EB150084 AT3G08690.1 9e-27 ubiquitin-conjugating enzyme 11 (UBC11), E2
213416 EB157314 AT1G62990.1 1e-126 homeodomain transcription factor (KNAT7)
220588 EB132350 AT3G48590.1 2e-15 CCAAT-box binding transcription factor Hap5a, putative
220604 CN948726 AT4G33260.1 8e-17 WD-40 repeat family protein
245977 CN903005 AT3G26730.1 1e-49 zinc finger (C3HC4-type RING finger) family protein
256235 CN913864 AT2G31320.1 0 NAD(+) ADP-ribosyltransferase, putative
256449 CN916743 AT3G22890.1 1e-165 sulfate adenylyltransferase 1/ATP-sulfurylase 1 (APS1)
257853 CN914478 AT5G52640.1 0 heat shock protein 81-1 (HSP81-1)
261756 CN908391 AT2G25050.1 5e-07 formin homology 2 domain-containing protein
264654 CN910347 AT5G67100.1 5e-87 DNA-directed DNA polymerase α catalytic subunit, putative
265667 CN910570 AT5G16270.1 3e-06 Rad21/Rec8-like family protein
266414 EB152178 AT5G40010.1 1e-112 AAA-type ATPase family protein
315707 CN915704 AT1G03080.1 4e-25 kinase interacting family protein
318786 CN949202 AT1G04820.1 4e-63 tubulin α-2/α-4 chain (TUA4)
Mid dev cluster
EST Genbank acc. Best A. thaliana hit e value Description
109011 CN880656 AT1G29400.1 4e-77 RNA recognition motif (RRM)-containing protein
144884 CN894104 AT1G03190.1 1e-33 DNA repair protein/transcription factor protein (UVH6)
146572 CN895134 AT2G15580.1 2e-14 zinc finger (C3HC4-type RING finger) family protein
167024 EG631355 AT5G66770.1 0 scarecrow transcription factor family protein
182020 EB143575 AT1G69840.1 3e-73 band 7 family protein
185452 EB148668 AT1G07350.1 1e-31 transformer serine/arginine-rich ribonucleoprotein, putative
214774 CN946063 AT1G26830.1 1e-75 CUL3 Cullin, putative, similar to Cullin homolog 3 (CUL-3)
268033 CN918413 AT5G64610.1 1e-142 histone acetyltransferase, putative
Ripening cluster
EST Genbank acc. Best A. thaliana hit e value Description
541 CN934040 AT3G57220.1 1e-113 UDP-GlcNAc:dolichol phosphate N-acetylglucosamine-1-phosphate transferase, putative,
11629 EB109003 AT1G34260.1 1e-07 phosphatidylinositol-4-phosphate 5-kinase family protein
15678 CN932487 AT5G51600.1 3e-85 microtubule associated protein (MAP65/ASE1) family protein
57477 CN860296 AT2G44270.1 1e-164 contains Pfam profile PF01171: PP-loop family
59442 CN862410 AT1G73460.1 1e-35 protein kinase family protein Pfam:PF00069
64262 CN850169 AT2G30200.1 1e-148 expressed protein T27E13_6
64821 CN863160 AT5G51570.1 1e-141 band 7 family protein
68274 CN864737 AT5G26940.1 3e-59 exonuclease family protein
89547 CN873630 AT3G61140.1 2e-09 COP9 signalosome complex subunit 1/CSN complex subunit 1
89732 EB121320 AT4G12600.1 8e-18 ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein
93568 CN874587 AT3G10940.1 1e-108 similar to protein phosphatase PTPKIS1 protein
107778 CN871562 AT1G77600.1 6e-07 expressed protein, weak similarity to Pds5
111901 CN879476 AT1G14400.1 1e-39 ubiquitin-conjugating enzyme 1 (UBC1), E2
130406 CN891639 AT3G27180.1 5e-08 expressed protein MYF5.5
132758 CN892125 AT5G48330.1 9e-55 regulator of chromosome condensation (RCC1) family protein
134470 CN888599 AT2G29900.1 2e-35 presenilin family protein
141926 CN939221 AT5G50960.1 1e-163 similar to Nucleotide-binding protein 1 (NBP 1)
143463 CN890171 AT1G69670.1 9e-75 ATCUL3B cullin, putative
146658 CN895184 AT5G12200.1 0 dihydropyrimidinase (PYD2)
147359 EB138102 AT1G05910.1 1e-111 cell division cycle protein 48-related/CDC48-related
147418 CN895629 AT3G18600.1 4e-32 DEAD/DEAH box helicase, putative
150678 CN898212 AT3G07760.1 3e-28 expressed protein MLP3.21
155382 CN901049 AT3G24320.1 3e-73 DNA mismatch repair MutS family (MSH1)
159868 EB128540 AT2G19770.1 5e-45 profilin 4 (PRO4) (PFN4)
172304 CN883582 AT3G48530.1 2e-72 CBS domain-containing protein
175286 CN904072 AT4G25130.1 1e-100 peptide methionine sulfoxide reductase, putative
184340 EB147575 AT3G13230.1 2e-77 expressed protein MDC11.5
185727 EB148939 AT5G21990.1 1e-107 tetratricopeptide repeat (TPR)-containing protein
186037 EB149246 AT4G25130.1 3e-71 peptide methionine sulfoxide reductase, putative
216840 CN947326 AT4G04955.1 3e-45 ATALN Encodes an allantoinase
219785 CN851874 AT2G30200.1 1e-148 expressed protein T27E13_6
221777 CN875931 AT5G17570.1 1e-115 tatD-related deoxyribonuclease family protein
221885 EB122552 AT1G55860.1 2e-19 ubiquitin-protein ligase 1 (UPL1)
225203 CN877466 AT1G68370.1 9e-74 gravity-responsive protein (ARG1)
228881 CN878128 AT1G77930.1 1e-105 DNAJ heat shock N-terminal domain-containing protein
229438 CN878271 AT1G20760.1 2e-30 calcium-binding EF hand family protein
229922 CN878558 AT1G20110.1 4e-73 zinc finger (FYVE type) family protein
257846 CN914471 AT1G15240.1 8e-26 phox (PX) domain-containing protein
266842 CN916307 AT2G45620.1 4e-09 nucleotidyltransferase family protein
267005 CN916212 AT4G28000.1 7e-51 AAA-type ATPase family protein
267748 CN918233 AT5G41370.1 4e-13 XPB1 involved in both DNA repair and transcription
289972 CN884487 AT3G23610.1 5e-60 dual specificity protein phosphatase (DsPTP1)
  1. a ESTs that change during fruit development were used to identify apple genes and the best Arabidopsis homolog (by BLAST) was found for that apple gene. Where a sequence similarity was better than 1 × e-5 the MIPS functional category for that Arabidopsis gene was determined.
  2. b Genes with the functional category "Cell cycle and DNA processing" were identified in each array cluster and ESTs in those clusters and the annotation of the Arabidopsis homolog is shown.