Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.19.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8502	0.456
27DAP/17DAP	0.8955	0.764
39DAP/27DAP	1.16802	0.779
41DAP/39DAP	1.02776	0.921
42DAP/41DAP	1.02636	1
43DAP/42DAP	1.0655	1
47DAP/43DAP	1.09383	0.856
52DAP/47DAP	0.82428	0.548
57DAP/52DAP	0.98179	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34249	0.049
17DAP/reference	1.37271	0.047
27DAP/reference	1.38653	0.013
39DAP/reference	1.43407	0.02
41DAP/reference	1.43545	0.013
42DAP/reference	1.36465	0.001
43DAP/reference	1.20945	0.017
47DAP/reference	1.64319	0.001
52DAP/reference	1.61145	0.008
57DAP/reference	1.30181	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12914	0.205
27DAP/17DAP	0.97931	0.782
39DAP/27DAP	0.86963	0.121
41DAP/39DAP	1.08883	0.55
42DAP/41DAP	0.96487	0.687
43DAP/42DAP	1.01274	0.627
47DAP/43DAP	1.06517	0.664
52DAP/47DAP	1.0468	0.804
57DAP/52DAP	0.95553	0.498
57DAP/7DAP	0.90563	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24189
17DAP/reference	N/A	N/A
27DAP/reference	1.56468
39DAP/reference	N/A	N/A
41DAP/reference	1.21257	0.012
42DAP/reference	1.47991
43DAP/reference	1.23397	0.007
47DAP/reference	1.66119	0.149
52DAP/reference	2.38866	0.121
57DAP/reference	1.64743	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13844	0.62
17DAP/reference	1.38761	0.025
27DAP/reference	1.3711	0.014
39DAP/reference	1.38854	0.016
41DAP/reference	1.60232	0.005
42DAP/reference	1.22601	0.072
43DAP/reference	1.39546	0.009
47DAP/reference	1.25991	0.009
52DAP/reference	1.27867	0.03
57DAP/reference	1.0621	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01278	1
17DAP/reference	1.17759	0.317
27DAP/reference	1.72979	0.025
39DAP/reference	1.65988	0.022
41DAP/reference	1.57559	0.047
42DAP/reference	2.05333	0.007
43DAP/reference	1.40483	0.046
47DAP/reference	1.15571	0.093
52DAP/reference	1.47633	0.068
57DAP/reference	1.64288	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.47732	0.966
26DAP/20DAP	0.90027	0.512
34DAP/26DAP	1.00932	1
51DAP/34DAP	0.99506	0.957
52DAP/51DAP	0.97041	1
53DAP/52DAP	0.8944	0.371
55DAP/53DAP	0.98428	0.807
57DAP/55DAP	0.98938	0.911
62DAP/57DAP	1.12366	0.902
68DAP/62DAP	1.23864	0.609
68DAP/14DAP	0.96075	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93598	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.43226	0.024
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.50455	0.293
Mature Eggplant/Ripe Tomato	3.55768	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90754	0.907
1-1-2/M82	1.09639	1
12-2/M82	0.8844	0.721
12-4/M82	0.91064	1
1-3/M82	N/A	N/A
2-1-1/M82	0.75383	0.92
2-1/M82	0.94978
2-6/M82	N/A	N/A
3-2/M82	0.89913	0.451
4-1-1/M82	N/A	N/A
4-1/M82	1.00619
4-3-2/M82	1.0083
4-3/M82	0.91955	1
5-3/M82	1.0568	1
6-2/M82	0.88025
6-3/M82	0.80151
7-1/M82	0.94605
7-2/M82	1.17724	0.385
9-3-2/M82	0.92483

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	0.94249
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.11861	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	1.02521	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01257	0.921
DC3000/delta hrp 6h	0.94295	0.95
DC3000/delta hrp 12h	1.13378	1
DC3000/delta hrp 24h	0.65717	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73773	0.093
DC3000 delta B/DC3000 delta AB	0.53391	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12374	1
Exp 36h	0.95434	0.82
Exp 60h	0.97731	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00305	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.86428	0.338
Var 12h NI row2-row1	0.89862	0.36
Var 36h I row2-row1	0.95685	1
Var 36h NI row2-row1	1.10175	0.482
Var 60h I row2-row1	1.1773	0.543
Var 60h NI row2-row1	1.08455	0.904
Time course 0hI-0hNI	1.00368	1
Time course 12hI-12hNI	0.98504	0.924
Time course 36hI-36hNI	0.93468	0.246
Time course 60hI-60hNI	0.31972	0.006

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)	1.04713	0.511
transgenic ySAMdc/azygous control (breaker)	0.79503	0.132
transgenic ySAMdc/azygous control (red)	0.85778	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86883	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.24845	0.222

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)	1.02753	1