Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.20.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92973	0.689
27DAP/17DAP	1.05446	1
39DAP/27DAP	1.14383	0.732
41DAP/39DAP	0.87186	0.539
42DAP/41DAP	1.40825	0.412
43DAP/42DAP	1.03463	0.937
47DAP/43DAP	1.19632	0.405
52DAP/47DAP	0.81957	0.539
57DAP/52DAP	1.02605	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90387	0.371
17DAP/reference	0.98615	0.819
27DAP/reference	0.85568	0.295
39DAP/reference	0.92864	0.424
41DAP/reference	0.93032	0.434
42DAP/reference	0.80265	0.011
43DAP/reference	0.62475
47DAP/reference	0.81174	0.098
52DAP/reference	1.12309	0.607
57DAP/reference	0.68501

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92145	0.716
27DAP/17DAP	0.91528	0.887
39DAP/27DAP	0.69347
41DAP/39DAP	1.02681
42DAP/41DAP	1.53365	0.8
43DAP/42DAP	2.3314
47DAP/43DAP	1.32166	0.127
52DAP/47DAP	2.13121	0.081
57DAP/52DAP	0.74086
57DAP/7DAP	2.49133

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85525	0.122
17DAP/reference	0.95698	0.338
27DAP/reference	1.04775	1
39DAP/reference	0.89944	0.23
41DAP/reference	0.87953	0.271
42DAP/reference	0.93629	0.371
43DAP/reference	1.01013	0.58
47DAP/reference	0.89177	0.101
52DAP/reference	0.99396	0.621
57DAP/reference	1.14455	0.214

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88707	0.386
17DAP/reference	0.84655	0.201
27DAP/reference	0.67046	0.067
39DAP/reference	1.09815	1
41DAP/reference	0.63368	0.046
42DAP/reference	1.16409	1
43DAP/reference	0.86622	0.229
47DAP/reference	0.52617
52DAP/reference	0.92477	0.111
57DAP/reference	0.81697	0.02

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91578	0.335
17DAP/reference	0.91277	0.292
27DAP/reference	1.15569	0.062
39DAP/reference	1.01809	1
41DAP/reference	1.029	0.889
42DAP/reference	0.89968	0.22
43DAP/reference	0.96965	0.614
47DAP/reference	0.90852	0.097
52DAP/reference	1.49519	0.412
57DAP/reference	1.048	0.8

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14415	0.966
26DAP/20DAP	0.75007	1
34DAP/26DAP	0.94094	0.954
51DAP/34DAP	1.4514	0.044
52DAP/51DAP	1.02684
53DAP/52DAP	1.3101	0.868
55DAP/53DAP	1.52925	0.218
57DAP/55DAP	0.62227	0.061
62DAP/57DAP	1.3129	0.723
68DAP/62DAP	2.69734	0.017
68DAP/14DAP	2.47296	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68499	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.53832	0.031
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.17809
Mature Eggplant/Ripe Tomato	0.11011

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.97242	1
12-2/M82	N/A	N/A
12-4/M82	1.19027
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	1.12835
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	0.91172
6-2/M82	N/A	N/A
6-3/M82	1.00256
7-1/M82	1.17976
7-2/M82	0.77623
9-3-2/M82	0.86127

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.12754
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.16351
IL7-3/WTpooled	0.73925
IL12-4/WTpooled	1.08041	1
IL1-4/WTpooled	0.9107	0.834
WT/WTpooled	0.77788	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	0.89303

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.32074	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.40468	1
DC3000/delta hrp 24h	1.11187	0.62

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94023	1
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
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)	1.07044	0.612
transgenic ySAMdc/azygous control (breaker)	0.66982	0.131
transgenic ySAMdc/azygous control (red)	0.93108	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07872	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.80538	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87045	1
Manapal/WT (break)	0.86254	0.299
Manapal/WT (red)	1.30954	0.413