Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.6.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97137	0.779
27DAP/17DAP	1.1751	0.829
39DAP/27DAP	0.8827	0.522
41DAP/39DAP	1.28901	0.37
42DAP/41DAP	1.01154	1
43DAP/42DAP	1.01787	1
47DAP/43DAP	1.04718	0.95
52DAP/47DAP	0.90333	0.709
57DAP/52DAP	1.03892	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95729	0.432
17DAP/reference	0.91348	0.104
27DAP/reference	0.92793	0.157
39DAP/reference	0.97488	0.762
41DAP/reference	0.82364	0.012
42DAP/reference	1.20832	0.003
43DAP/reference	1.10405	0.013
47DAP/reference	1.03863	0.509
52DAP/reference	0.98557	0.58
57DAP/reference	0.95646	0.138

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89431	0.56
27DAP/17DAP	1.0181	0.968
39DAP/27DAP	1.12152	0.429
41DAP/39DAP	0.94465	0.923
42DAP/41DAP	1.10855	0.2
43DAP/42DAP	1.19446	0.042
47DAP/43DAP	0.9925	0.971
52DAP/47DAP	0.82693	0.064
57DAP/52DAP	0.9862	0.793
57DAP/7DAP	0.88117	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.64117	0.047
17DAP/reference	1.19177	0.049
27DAP/reference	1.23682	0.018
39DAP/reference	1.05813	0.779
41DAP/reference	0.9664	0.589
42DAP/reference	1.10752	0.686
43DAP/reference	1.02417	0.764
47DAP/reference	1.42005	0.027
52DAP/reference	1.38156	0.019
57DAP/reference	1.23793	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99577	0.884
17DAP/reference	0.92066	0.287
27DAP/reference	1.33401	0.046
39DAP/reference	1.00966	1
41DAP/reference	1.02446	1
42DAP/reference	1.0402	0.81
43DAP/reference	0.70816	0.013
47DAP/reference	0.84288	0.01
52DAP/reference	0.78285	0.003
57DAP/reference	0.72594	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13888	0.518
17DAP/reference	0.86904	0.335
27DAP/reference	0.83455
39DAP/reference	0.88739	0.36
41DAP/reference	1.17096	0.15
42DAP/reference	1.43625	0.154
43DAP/reference	1.79038	0.032
47DAP/reference	0.88088	0.049
52DAP/reference	1.17614	0.631
57DAP/reference	1.17555	0.192

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00207	1
26DAP/20DAP	0.94138	0.223
34DAP/26DAP	1.05341	0.819
51DAP/34DAP	1.02035	0.909
52DAP/51DAP	0.93284	0.151
53DAP/52DAP	1.01848	0.858
55DAP/53DAP	1.00237	0.964
57DAP/55DAP	1.08077	0.779
62DAP/57DAP	0.99349	1
68DAP/62DAP	1.22755	0.206
68DAP/14DAP	1.42261	0.035

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.22807	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.6515	0.165
Mature Green Tomato/Ripe Tomato	1.00673	1
Immature Eggplant/Mature Eggplant	1.37718	0.05
Ripe Pepper/Ripe Tomato	0.94786	1
Mature Eggplant/Ripe Tomato	1.54211	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92734	0.934
1-1-2/M82	1.04445	1
12-2/M82	0.96861	0.955
12-4/M82	0.94251	1
1-3/M82	1.02966	1
2-1-1/M82	0.96384	0.92
2-1/M82	1.17927	1
2-6/M82	0.97396	1
3-2/M82	0.90826	1
4-1-1/M82	0.93848	1
4-1/M82	1.01711	1
4-3-2/M82	0.96499	1
4-3/M82	1.02961	1
5-3/M82	0.98908	1
6-2/M82	1.01424	1
6-3/M82	1.0073	1
7-1/M82	1.03124	1
7-2/M82	1.02892	1
9-3-2/M82	0.79278	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06691	1
IL2-6/WTpooled	1.2158	0.659
IL7-5/WTpooled	1.0214
IL7-3/WTpooled	0.86967	0.418
IL12-4/WTpooled	0.90606	0.71
IL1-4/WTpooled	1.03483	1
WT/WTpooled	0.95556	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.24305	0.167

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01308	0.921
DC3000/delta hrp 6h	0.83876	0.95
DC3000/delta hrp 12h	1.04559	1
DC3000/delta hrp 24h	0.97395	0.861

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79475	0.028
DC3000 delta B/DC3000 delta AB	0.82266	0.041

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9617	1
Exp 36h	1.10627	1
Exp 60h	0.98647	0.994

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.99794	1
Var 0h	1.36722	0.305
Var 12h I row2-row1	0.93724	0.565
Var 12h NI row2-row1	0.96818	0.906
Var 36h I row2-row1	0.87313	0.575
Var 36h NI row2-row1	1.15805	1
Var 60h I row2-row1	1.05313	1
Var 60h NI row2-row1	0.98311	1
Time course 0hI-0hNI	1.00142	1
Time course 12hI-12hNI	0.96706	0.698
Time course 36hI-36hNI	0.83429	0.042
Time course 60hI-60hNI	0.51534	0.006

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.12252	0.612
transgenic ySAMdc/azygous control (breaker)	0.82007	0.134
transgenic ySAMdc/azygous control (red)	0.96824	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.14109	0.057

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.04848	1

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05548	1
Manapal/WT (break)	1.33863	0.13
Manapal/WT (red)	0.838	0.184