Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98358	0.752
27DAP/17DAP	1.01885	0.863
39DAP/27DAP	1.02038	0.782
41DAP/39DAP	0.92981	0.815
42DAP/41DAP	0.92431	1
43DAP/42DAP	0.99013	0.925
47DAP/43DAP	1.10779	0.776
52DAP/47DAP	1.08806	0.856
57DAP/52DAP	1.73705	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24477	0.421
17DAP/reference	1.02992	0.874
27DAP/reference	1.07203	0.587
39DAP/reference	0.98604	0.816
41DAP/reference	0.88716	0.267
42DAP/reference	0.87813	0.009
43DAP/reference	1.0198	0.899
47DAP/reference	0.95557	0.3
52DAP/reference	0.87578	0.017
57DAP/reference	0.97754	0.435

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.37379	0.192
27DAP/17DAP	0.97646	0.887
39DAP/27DAP	1.05433	0.718
41DAP/39DAP	1.20908	0.304
42DAP/41DAP	0.93588	0.491
43DAP/42DAP	1.21942	0.351
47DAP/43DAP	1.05848	1
52DAP/47DAP	0.81873	0.226
57DAP/52DAP	0.8693	0.546
57DAP/7DAP	1.25555	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01676	0.758
17DAP/reference	0.90521	0.124
27DAP/reference	0.89976	0.109
39DAP/reference	0.92059	0.264
41DAP/reference	0.97315	0.489
42DAP/reference	0.8919	0.248
43DAP/reference	0.85912	0.046
47DAP/reference	0.89734	0.671
52DAP/reference	0.86102	0.15
57DAP/reference	0.94145	0.291

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93737	0.564
17DAP/reference	0.83086	0.164
27DAP/reference	0.9242	0.407
39DAP/reference	0.97258	0.497
41DAP/reference	1.04337	0.601
42DAP/reference	0.81892	0.108
43DAP/reference	0.81657	0.114
47DAP/reference	0.85104	0.284
52DAP/reference	0.65538	0.003
57DAP/reference	0.82877	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95973	0.489
17DAP/reference	0.9206	0.426
27DAP/reference	0.96906	0.465
39DAP/reference	0.97032	0.43
41DAP/reference	0.95531	0.512
42DAP/reference	0.82232	0.172
43DAP/reference	0.75542	0.035
47DAP/reference	0.82403	0.012
52DAP/reference	0.82595	0.164
57DAP/reference	0.88964	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.33108	0.966
26DAP/20DAP	0.83457	1
34DAP/26DAP	1.38766	0.819
51DAP/34DAP	N/A	N/A
52DAP/51DAP	1.18124
53DAP/52DAP	1.02528	1
55DAP/53DAP	1.2532	0.771
57DAP/55DAP	1.1218	0.923
62DAP/57DAP	0.74665	0.681
68DAP/62DAP	1.1977	0.759
68DAP/14DAP	1.44486	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79735	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.99544
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12541
1-1-2/M82	1.19307
12-2/M82	N/A	N/A
12-4/M82	0.95347
1-3/M82	N/A	N/A
2-1-1/M82	1.20013	0.338
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	0.80058	0.364
6-2/M82	N/A	N/A
6-3/M82	1.17302
7-1/M82	N/A	N/A
7-2/M82	0.99349
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.75714	0.243
IL2-6/WTpooled	1.01912	0.659
IL7-5/WTpooled	0.98232	1
IL7-3/WTpooled	0.57407	0.294
IL12-4/WTpooled	0.81923	0.71
IL1-4/WTpooled	0.91022	0.834
WT/WTpooled	0.97657	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	1.0674	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90032	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.43408	0.151

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	N/A	N/A
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	1.03712
Var 0h	1.14429	0.98
Var 12h I row2-row1	1.13893
Var 12h NI row2-row1	0.87557
Var 36h I row2-row1	0.85364
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	0.95684
Var 60h NI row2-row1	0.68626	0.904
Time course 0hI-0hNI	0.95547	0.812
Time course 12hI-12hNI	0.76728
Time course 36hI-36hNI	1.21911	0.453
Time course 60hI-60hNI	0.85389	0.646

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)	1.34867	0.798
transgenic ySAMdc/azygous control (breaker)	1.48259	1
transgenic ySAMdc/azygous control (red)	1.09526	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94885	0.038

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.91168	0.503