Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.12.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.28879	0.739
27DAP/17DAP	0.56715	0.042
39DAP/27DAP	0.69602	0.512
41DAP/39DAP	1.3401	0.498
42DAP/41DAP	0.83841	1
43DAP/42DAP	1.84299	0.265
47DAP/43DAP	0.99678	0.699
52DAP/47DAP	1.08153	0.848
57DAP/52DAP	1.15943	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.43143	0.03
17DAP/reference	0.48578	0.007
27DAP/reference	0.54555	0.011
39DAP/reference	1.36358	0.8
41DAP/reference	0.74631	0.065
42DAP/reference	2.50519	0.001
43DAP/reference	5.62518	0.006
47DAP/reference	5.91747	0.001
52DAP/reference	2.4538	0.008
57DAP/reference	3.37322	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.82047
27DAP/17DAP	1.23734
39DAP/27DAP	1.3923	0.862
41DAP/39DAP	N/A	N/A
42DAP/41DAP	1.1519	1
43DAP/42DAP	1.53419
47DAP/43DAP	1.00935	0.961
52DAP/47DAP	0.53443	0.112
57DAP/52DAP	1.4561	0.368
57DAP/7DAP	2.85269

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74159	0.073
17DAP/reference	0.91001	0.082
27DAP/reference	0.86903	0.2
39DAP/reference	0.79606	0.073
41DAP/reference	0.8044	0.122
42DAP/reference	0.81486	0.031
43DAP/reference	0.87619	0.166
47DAP/reference	0.79977	0.168
52DAP/reference	0.98632	0.571
57DAP/reference	0.8558	0.176

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.476	0.008
17DAP/reference	0.3682	0.006
27DAP/reference	0.4143	0.008
39DAP/reference	0.44293	0.008
41DAP/reference	0.50302	0.009
42DAP/reference	0.48253	0.012
43DAP/reference	0.5888	0.009
47DAP/reference	1.32965	0.658
52DAP/reference	0.34007	0.003
57DAP/reference	0.57885	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62674	0.045
17DAP/reference	0.91569	0.433
27DAP/reference	0.84729	0.195
39DAP/reference	1.01026	0.693
41DAP/reference	0.90764	0.264
42DAP/reference	1.49223	0.214
43DAP/reference	2.31391	0.07
47DAP/reference	5.001	0.005
52DAP/reference	1.15365	0.566
57DAP/reference	2.23165	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00231	1
26DAP/20DAP	1.97054	0.144
34DAP/26DAP	1.9264
51DAP/34DAP	N/A	N/A
52DAP/51DAP	0.82097
53DAP/52DAP	1.02834	0.97
55DAP/53DAP	0.76467
57DAP/55DAP	1.10921	0.779
62DAP/57DAP	0.08366	0.002
68DAP/62DAP	0.65238	0.056
68DAP/14DAP	1.76738

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.55056

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.38925
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	3.5007	0.05
Ripe Pepper/Ripe Tomato	0.07152	0.224
Mature Eggplant/Ripe Tomato	0.03071

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	0.981
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.88573	1
IL12-4/WTpooled	1.1678	0.646
IL1-4/WTpooled	0.83068	0.562
WT/WTpooled	1.06957	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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	2.52976
DC3000/delta hrp 12h	0.83984	1
DC3000/delta hrp 24h	N/A	N/A

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	0.79133	1
Exp 36h	1.00456	0.943
Exp 60h	1.1753	1

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	1.12022	0.594
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)	0.80529	0.428
transgenic ySAMdc/azygous control (breaker)	1.09444	1
transgenic ySAMdc/azygous control (red)	1.07159	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07001	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.30616	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.78229	0.096
Manapal/WT (break)	1.06887	0.381
Manapal/WT (red)	1.10108	1