Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.10.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89677	0.395
27DAP/17DAP	0.84137	0.561
39DAP/27DAP	0.93047	0.544
41DAP/39DAP	0.73638	0.126
42DAP/41DAP	1.15835	0.825
43DAP/42DAP	1.18398	0.861
47DAP/43DAP	0.93588	0.76
52DAP/47DAP	0.84399	0.593
57DAP/52DAP	0.91957	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3383	0.025
17DAP/reference	1.0838	0.631
27DAP/reference	0.95332	0.514
39DAP/reference	0.96406	0.587
41DAP/reference	0.788	0.021
42DAP/reference	1.10427	0.076
43DAP/reference	0.87671	0.107
47DAP/reference	1.07763	0.646
52DAP/reference	0.95408	0.393
57DAP/reference	1.03241	0.511

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27484	0.151
27DAP/17DAP	0.78154	0.121
39DAP/27DAP	0.63406	0.068
41DAP/39DAP	1.25517	0.19
42DAP/41DAP	1.13654	0.694
43DAP/42DAP	0.82217	0.045
47DAP/43DAP	1.00402	0.989
52DAP/47DAP	0.93354	0.729
57DAP/52DAP	1.04491	0.957
57DAP/7DAP	0.45181	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.14086	0.025
17DAP/reference	3.65973	0.006
27DAP/reference	4.10619	0.006
39DAP/reference	4.39291	0.005
41DAP/reference	4.56419	0.008
42DAP/reference	4.88398	0.006
43DAP/reference	5.79516	0.006
47DAP/reference	3.07529	0.13
52DAP/reference	4.76394	0.007
57DAP/reference	3.00517	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.45043	0.21
17DAP/reference	1.34844	0.015
27DAP/reference	1.12798	0.552
39DAP/reference	1.2381	0.657
41DAP/reference	0.99182	0.557
42DAP/reference	1.01064	1
43DAP/reference	1.14143	1
47DAP/reference	0.9237	0.188
52DAP/reference	1.05257	1
57DAP/reference	0.70988	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.61837	0.015
17DAP/reference	2.05596	0.166
27DAP/reference	3.41814	0.015
39DAP/reference	3.62672	0.005
41DAP/reference	3.62443	0.006
42DAP/reference	3.44361	0.007
43DAP/reference	4.0416	0.006
47DAP/reference	1.32437	0.066
52DAP/reference	3.7134	0.035
57DAP/reference	2.57331	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09157	0.966
26DAP/20DAP	1.22173	1
34DAP/26DAP	0.9745	0.954
51DAP/34DAP	1.36636	0.496
52DAP/51DAP	0.73304	1
53DAP/52DAP	1.21491	0.806
55DAP/53DAP	0.78465	0.225
57DAP/55DAP	1.0079	0.997
62DAP/57DAP	0.87849	0.681
68DAP/62DAP	2.01066	0.142
68DAP/14DAP	0.86759

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.95618	0.52

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.09114	0.417
Mature Green Tomato/Ripe Tomato	2.54836	0.015
Immature Eggplant/Mature Eggplant	0.72823	0.062
Ripe Pepper/Ripe Tomato	7.69687	0.256
Mature Eggplant/Ripe Tomato	2.21796	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90707
1-1-2/M82	0.85759
12-2/M82	0.60889	0.639
12-4/M82	0.76244	0.33
1-3/M82	0.89389
2-1-1/M82	1.00158	1
2-1/M82	0.67786
2-6/M82	1.27083	0.505
3-2/M82	0.7852
4-1-1/M82	1.0533	1
4-1/M82	0.75164
4-3-2/M82	1.66063
4-3/M82	0.85979	0.611
5-3/M82	1.1232	1
6-2/M82	N/A	N/A
6-3/M82	1.02678	1
7-1/M82	1.02212	1
7-2/M82	1.04593
9-3-2/M82	1.12676	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.21936	0.419
IL7-5/WTpooled	1.20805
IL7-3/WTpooled	0.90211	1
IL12-4/WTpooled	0.94461	1
IL1-4/WTpooled	1.05877	1
WT/WTpooled	0.99089	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	1.12745	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93136	1
DC3000/delta hrp 6h	1.04176	1
DC3000/delta hrp 12h	0.96595	1
DC3000/delta hrp 24h	0.65987	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.56878	0.041
DC3000 delta B/DC3000 delta AB	0.54641	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.83598	1
Exp 36h	0.72766	0.589
Exp 60h	2.18127	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03307	1
Var 0h	0.96112	1
Var 12h I row2-row1	0.76071	0.338
Var 12h NI row2-row1	0.91874	0.82
Var 36h I row2-row1	0.99242	1
Var 36h NI row2-row1	1.17398	1
Var 60h I row2-row1	1.41793	1
Var 60h NI row2-row1	0.97942	1
Time course 0hI-0hNI	0.98274	0.955
Time course 12hI-12hNI	0.95185	0.515
Time course 36hI-36hNI	0.79987	0.023
Time course 60hI-60hNI	0.13644	0.005

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)	1.11158	0.326
transgenic ySAMdc/azygous control (breaker)	1.2527	0.248
transgenic ySAMdc/azygous control (red)	1.05217	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.81776	0.052

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.08416	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.84548	0.083
Manapal/WT (break)	1.94602	0.13
Manapal/WT (red)	2.57179	0.133