Table I. Selected genes affected by HDA6 in microarray analysis.
| Gene Name | Arabidopsis Genome Initiative Code | Ratioa | P | Description |
| Genes involved in flowering | ||||
| MAF4b | AT5G65070 | 12.2 | 1.00E-05 | MADS box protein, negative regulator of flowering |
| FLCb | AT5G10140 | 8.6 | 1.00E-05 | MADS box protein, negative regulator of flowering |
| MAF5b | AT5G65080 | 7.6 | 1.30E-03 | MADS box protein, negative regulator of flowering |
| AGP24b | AT5G40738 | 6.2 | 1.00E-05 | Most highly expressed in pollen |
| AT1G52000 | AT1G52000 | 3.5 | 1.00E-05 | Flower development |
| AT5G38440 | AT5G38440 | 3.5 | 4.90E-02 | Self-incompatibility protein relative |
| AT3G17010 | AT3G17010 | 3.4 | 1.40E-03 | Expressed in stamen primordia |
| OPR3 | AT2G06050 | 3.2 | 1.00E-04 | Male sterile and pollen dehiscence |
| ARPN | AT2G02850 | 2.3 | 3.00E-04 | Involved in anther development and pollination |
| SMZb | AT3G54990 | 2.3 | 1.00E-05 | AP2 domain transcription factor |
| UNE18 | AT5G02100 | 2.3 | 1.00E-05 | Double fertilization forming |
| MBP2 | AT1G52030 | 2.1 | 1.00E-04 | Flower development |
| AGL8b | AT5G60910 | −3.2 | 5.00E-04 | Positive regulation of flower development |
| SPL5 | AT3G15270 | −2.5 | 1.40E-03 | Involved in regulation of flowering |
| SOC1b | AT2G45660 | −2.4 | 1.25E-02 | Promotes flowering |
| FTb | AT1G65480 | −2.3 | 1.10E-03 | Promotes flowering |
| AT1G04770 | AT1G04770 | −2.1 | 1.00E-05 | Male sterility MS5 family protein |
| HAT2 | AT5G47370 | −1.8 | 1.40E-03 | Homeobox-Leu zipper genes |
| Genes involved in gene silencing | ||||
| AGO5b | AT2G27880 | 12.4 | 4.30E-03 | Similar to AGO1 (ARGONAUTE1) |
| AGO3b | AT1G31290 | 5.8 | 3.80E-03 | Similar to AGO2 (ARGONAUTE2) |
| HIS1-3b | AT2G18050 | 3.7 | 1.00E-05 | HISTONE 1H-3 |
| AT1G16705b | AT1G16705 | 3.5 | 1.73E-02 | P300/CBP acetyltransferase-related protein |
| AT5G64572 | AT5G64572 | 2.4 | 1.00E-04 | Potential natural antisense gene |
| AT1G63080b | AT1G63080 | 2.3 | 2.50E-02 | Transacting siRNA-generating locus |
| DMT7b | AT5G14620 | 2.1 | 3.69E-02 | Putative DNA methyltransferase |
| AT4G08590b | AT4G08590 | 2.1 | 3.00E-03 | Similar to VIM1 |
| AT2G33815 | AT2G33815 | −2.6 | 7.00E-04 | Potential natural antisense gene |
| Transposons | ||||
| AT5G59620b | AT5G59620 | 25.8 | 1.00E-05 | CACTA-like transposase family |
| AT2G04770b | AT2G04770 | 16.1 | 1.00E-05 | CACTA-like transposase family |
| AT5G30450 | AT5G30450 | 9.4 | 5.00E-04 | CACTA-like transposase family |
| AT5G19015b | AT5G19015 | 6.7 | 3.10E-03 | CACTA-like transposase family |
| AT3G29650 | AT3G29650 | 4 | 4.63E-02 | CACTA-like transposase family |
| AT4G09480b | AT4G09480 | 12.7 | 1.00E-05 | Copia-like retrotransposon family |
| AT2G20460b | AT2G20460 | 6.6 | 3.00E-04 | Copia-like retrotransposon family |
| AT4G09540b | AT4G09540 | 6.1 | 2.97E-02 | Copia-like retrotransposon family |
| AT2G11140 | AT2G11140 | 5.7 | 4.85E-02 | Copia-like retrotransposon family |
| AT2G26630b | AT2G26630 | 8.6 | 7.00E-04 | Transposase IS4 family protein |
| AT1G42705b | AT1G42705 | 6.5 | 2.24E-02 | hAT-like transposase family |
| AT2G04460b | AT2G04460 | 40.8 | 1.00E-04 | Similar to pol polyprotein |
| AT1G47860 | AT1G47860 | 3.8 | 3.11E-02 | Non-LTR retrotransposon family |
| AT4G03790 | AT4G03790 | 3 | 1.60E-03 | Gypsy-like retrotransposon family |
| Genes related to stress | ||||
| TET9b | AT4G30430 | 8.1 | 1.00E-04 | Involved in aging |
| AT3G10200b | AT3G10200 | 6.6 | 3.50E-02 | Dehydration-responsive protein-related |
| AT2G29500b | AT2G29500 | 3.3 | 1.00E-05 | Class I small heat shock protein (HSP17.6B-CI) |
| SRG1b | AT1G17020 | 3.1 | 2.64E-02 | Senescence-related gene |
| ATCLH1b | AT1G19670 | 2.3 | 2.74E-02 | Chlorophyll degradation and response to stress |
| ADR1b | AT1G33560 | 2.3 | 1.00E-05 | Encodes a NBS-LRR disease resistance protein |
| AOC1b | AT3G25760 | 2.2 | 3.15E-02 | JA biosynthesis |
| ATCXE18 | AT5G23530 | 2.2 | 1.98E-02 | Similar to ATGID1C/GID1C |
| JAZ7b | AT2G34600 | −5.1 | 1.20E-03 | JA signaling |
| STZb | AT1G27730 | −3.9 | 9.00E-04 | Salt tolerance |
| RHL41b | AT5G59820 | −3.2 | 1.41E-02 | Cold stress |
| CBF1 | AT4G25490 | −2.7 | 1.40E-03 | Cold stress |
| CBF2 | AT4G25470 | −3.1 | 1.00E-04 | Cold stress |
| Transcription factors | ||||
| AT1G59930b | AT1G59930 | 17.3 | 1.00E-05 | MADS box protein |
| AGL37b | AT1G65330 | 13.3 | 1.00E-05 | Type 1 MADS box protein |
| AT2G36080b | AT2G36080 | 3.9 | 3.17E-02 | B3 DNA-binding domain transcription factor |
| AT3G53370b | AT3G53370 | 3.5 | 1.00E-04 | DNA-binding S1FA family protein |
| AT5G66980b | AT5G66980 | 3.3 | 1.00E-05 | Transcriptional factor B3 family protein |
| AT5G25810b | AT5G25810 | 2.4 | 2.06E-02 | ERF/AP2 transcription factor family |
| AT1G74930b | AT1G74930 | −7.2 | 1.00E-05 | A member of the DREB subfamily A-5 of ERF/AP2 |
| AT5G61600b | AT5G61600 | −4 | 4.00E-04 | Encodes a member of the ERF |
| AT5G51190b | AT5G51190 | −3 | 2.70E-02 | Encodes a member of the ERF |
a
Expression fold increase or decrease in HDA6-RNAi (cs24039) relative to the Ws wild type.
b
Confirmed by quantitative real-time PCR.