Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.3.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.56913	0.049
27DAP/17DAP	2.4103	0.087
39DAP/27DAP	2.53852	0.045
41DAP/39DAP	0.73686	0.163
42DAP/41DAP	1.51945	0.223
43DAP/42DAP	1.25833	0.861
47DAP/43DAP	3.8061	0.197
52DAP/47DAP	0.96554	0.746
57DAP/52DAP	1.30733	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63713	0.024
17DAP/reference	0.69778	0.018
27DAP/reference	1.19638	0.026
39DAP/reference	0.98186	0.885
41DAP/reference	1.07043	0.667
42DAP/reference	1.25787	0.022
43DAP/reference	1.44698	1
47DAP/reference	2.53382	0.001
52DAP/reference	3.4247	0.007
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.5707	0.058
27DAP/17DAP	0.64944	0.134
39DAP/27DAP	5.15888	0.036
41DAP/39DAP	0.46769	0.023
42DAP/41DAP	1.59454	0.005
43DAP/42DAP	1.47272	0.026
47DAP/43DAP	1.0641	0.844
52DAP/47DAP	1.34546	0.414
57DAP/52DAP	1.59713	0.05
57DAP/7DAP	3.83206	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91862	0.445
17DAP/reference	0.85301	0.108
27DAP/reference	1.09548	0.453
39DAP/reference	1.25093	0.222
41DAP/reference	1.08462	0.577
42DAP/reference	1.01473	0.791
43DAP/reference	0.78755	0.019
47DAP/reference	1.28705	0.304
52DAP/reference	1.14329	0.229
57DAP/reference	0.9523	0.353

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.6767	0.009
17DAP/reference	0.76426	0.006
27DAP/reference	0.96233	0.501
39DAP/reference	1.08842	0.705
41DAP/reference	0.9879	0.57
42DAP/reference	1.03778	0.744
43DAP/reference	0.72567	0.01
47DAP/reference	0.94162	0.149
52DAP/reference	0.98211	0.537
57DAP/reference	0.76425	0.144

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95538	0.455
17DAP/reference	1.40669	0.876
27DAP/reference	1.00043	0.763
39DAP/reference	0.93158	0.328
41DAP/reference	1.23005	0.222
42DAP/reference	1.13925	0.424
43DAP/reference	1.56236	0.028
47DAP/reference	2.67485	0.008
52DAP/reference	1.63034	0.08
57DAP/reference	6.09224	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.69333	0.966
26DAP/20DAP	1.12643	0.487
34DAP/26DAP	1.08656	1
51DAP/34DAP	1.75676	0.032
52DAP/51DAP	0.81668	0.151
53DAP/52DAP	0.95766	0.876
55DAP/53DAP	0.71195	0.028
57DAP/55DAP	0.9209	0.688
62DAP/57DAP	0.85487	0.681
68DAP/62DAP	1.24363	0.626
68DAP/14DAP	1.79587	0.055

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.67429	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70282	0.19
Mature Green Tomato/Ripe Tomato	0.27606	0.017
Immature Eggplant/Mature Eggplant	1.68572	0.05
Ripe Pepper/Ripe Tomato	0.18583	0.224
Mature Eggplant/Ripe Tomato	1.21028	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.85756
12-2/M82	N/A	N/A
12-4/M82	1.50465	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.05534	0.549
4-1-1/M82	N/A	N/A
4-1/M82	1.74046
4-3-2/M82	0.71736	0.698
4-3/M82	N/A	N/A
5-3/M82	1.11711
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.90588
7-2/M82	N/A	N/A
9-3-2/M82	1.40221	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.1746
IL2-6/WTpooled	1.07469	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.04953	1
IL12-4/WTpooled	1.00195	1
IL1-4/WTpooled	0.98884	1
WT/WTpooled	0.99098	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	1.19571	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97839	1
DC3000/delta hrp 6h	1.04545	1
DC3000/delta hrp 12h	1.10118	1
DC3000/delta hrp 24h	0.78112	0.129

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.5691	0.054

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.5948	1
Exp 36h	1.30515	0.693
Exp 60h	1.60773	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.18459	0.936
Var 12h I row2-row1	0.69876	0.353
Var 12h NI row2-row1	1.01918	1
Var 36h I row2-row1	0.84939	0.438
Var 36h NI row2-row1	1.10256	1
Var 60h I row2-row1	1.28141	0.543
Var 60h NI row2-row1	1.04512	1
Time course 0hI-0hNI	0.91831
Time course 12hI-12hNI	0.92595
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.87384	0.348
transgenic ySAMdc/azygous control (breaker)	0.63975	0.15
transgenic ySAMdc/azygous control (red)	1.0759	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.66311	0.026

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.85649	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16747	0.307
Manapal/WT (break)	1.19163	1
Manapal/WT (red)	1.48478	0.222