Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.12.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01979	0.975
27DAP/17DAP	0.75617	0.287
39DAP/27DAP	0.89298	0.549
41DAP/39DAP	0.88338	0.555
42DAP/41DAP	1.40569	0.679
43DAP/42DAP	0.85629	0.639
47DAP/43DAP	0.56233	0.074
52DAP/47DAP	0.80951	0.559
57DAP/52DAP	1.07226	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56337	0.006
17DAP/reference	1.01853	1
27DAP/reference	0.82293	0.147
39DAP/reference	0.74764	0.022
41DAP/reference	0.77598	0.085
42DAP/reference	0.95594	0.295
43DAP/reference	0.775	0.054
47DAP/reference	0.75643	0.001
52DAP/reference	0.68314	0.053
57DAP/reference	0.95948	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8285	0.158
27DAP/17DAP	1.08508	0.912
39DAP/27DAP	0.7564	0.181
41DAP/39DAP	1.54459	0.232
42DAP/41DAP	0.74648	0.109
43DAP/42DAP	0.80214	0.165
47DAP/43DAP	1.01924	0.971
52DAP/47DAP	1.19562	0.831
57DAP/52DAP	1.11562	0.917
57DAP/7DAP	0.63419	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.71044	0.025
17DAP/reference	1.48552	0.019
27DAP/reference	1.18839	0.014
39DAP/reference	1.13807	0.126
41DAP/reference	1.10797	0.336
42DAP/reference	1.02489	0.686
43DAP/reference	1.11206	0.188
47DAP/reference	0.94681	0.504
52DAP/reference	0.90181	0.061
57DAP/reference	1.06123	0.468

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35785	0.055
17DAP/reference	1.46165	0.007
27DAP/reference	1.15965	0.221
39DAP/reference	1.10177	0.764
41DAP/reference	1.00381	0.615
42DAP/reference	0.99039	0.594
43DAP/reference	0.93718	0.378
47DAP/reference	0.9512	0.261
52DAP/reference	0.8841	0.143
57DAP/reference	0.84611	0.058

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44301	0.015
17DAP/reference	1.47217	0.092
27DAP/reference	1.30069	0.028
39DAP/reference	1.24192	0.011
41DAP/reference	0.97098	0.56
42DAP/reference	0.95516	0.445
43DAP/reference	1.05091	1
47DAP/reference	0.73445	0.006
52DAP/reference	1.22763	0.614
57DAP/reference	0.69508	0.018

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97495	1
26DAP/20DAP	1.0855	0.896
34DAP/26DAP	0.88205	0.944
51DAP/34DAP	1.22087	0.936
52DAP/51DAP	0.80851	0.079
53DAP/52DAP	1.07774	0.868
55DAP/53DAP	1.10038	1
57DAP/55DAP	1.06878	0.935
62DAP/57DAP	1.02469	1
68DAP/62DAP	0.7348	0.345
68DAP/14DAP	0.9331	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.50571	0.064

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.13328	0.417
Mature Green Tomato/Ripe Tomato	11.619	0.015
Immature Eggplant/Mature Eggplant	0.7577	0.086
Ripe Pepper/Ripe Tomato	14.9802	0.256
Mature Eggplant/Ripe Tomato	14.964	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.85955
12-2/M82	N/A	N/A
12-4/M82	1.03906	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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	3.41384	0.427
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.26377	0.277
IL2-6/WTpooled	0.88154	1
IL7-5/WTpooled	0.84519	1
IL7-3/WTpooled	1.45145	1
IL12-4/WTpooled	1.04321	0.891
IL1-4/WTpooled	1.20743	0.426
WT/WTpooled	0.99343	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	0.93459	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05554	0.774
DC3000/delta hrp 6h	1.02217	1
DC3000/delta hrp 12h	1.01195	1
DC3000/delta hrp 24h	0.94691	0.654

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	1.19076	0.609

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95254	1
Exp 36h	1.16312	1
Exp 60h	0.76515	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01863	1
Var 0h	0.53818	1
Var 12h I row2-row1	0.84925	0.357
Var 12h NI row2-row1	0.9452	0.906
Var 36h I row2-row1	1.12929	0.601
Var 36h NI row2-row1	0.98596	0.791
Var 60h I row2-row1	1.07648	0.562
Var 60h NI row2-row1	1.08128	0.904
Time course 0hI-0hNI	1.00108	1
Time course 12hI-12hNI	0.95627	0.65
Time course 36hI-36hNI	1.02951	0.799
Time course 60hI-60hNI	1.12954	0.137

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)	1.01215	0.921
transgenic ySAMdc/azygous control (breaker)	0.53652	0.134
transgenic ySAMdc/azygous control (red)	1.60549	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94734	0.049

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82812	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91796	1
Manapal/WT (break)	0.64252	0.333
Manapal/WT (red)	0.87783	0.274