Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.2.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95496	0.689
27DAP/17DAP	0.87471	0.704
39DAP/27DAP	1.39923	0.135
41DAP/39DAP	0.65204	0.068
42DAP/41DAP	1.12677	0.894
43DAP/42DAP	0.91906	0.807
47DAP/43DAP	1.01951	0.949
52DAP/47DAP	1.04341	0.967
57DAP/52DAP	1.31641	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93088	0.224
17DAP/reference	0.90319	0.158
27DAP/reference	0.91232	0.369
39DAP/reference	0.87539	0.09
41DAP/reference	0.74769	0.039
42DAP/reference	0.73023	0.04
43DAP/reference	0.95607	0.728
47DAP/reference	0.8934	0.127
52DAP/reference	1.0337	0.84
57DAP/reference	1.02685	0.762

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9557	0.595
27DAP/17DAP	1.29581	0.154
39DAP/27DAP	0.92674	0.594
41DAP/39DAP	1.18538	0.674
42DAP/41DAP	1.05981	0.947
43DAP/42DAP	0.79246	0.034
47DAP/43DAP	1.07536	0.822
52DAP/47DAP	0.92388	0.777
57DAP/52DAP	0.99465	0.848
57DAP/7DAP	0.68306	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33396	0.091
17DAP/reference	1.04975	0.971
27DAP/reference	1.34401	0.088
39DAP/reference	1.28007	0.601
41DAP/reference	1.33059	0.041
42DAP/reference	1.00557	0.641
43DAP/reference	1.17797	0.188
47DAP/reference	1.13043	0.549
52DAP/reference	1.31016	0.149
57DAP/reference	1.13553	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90917	0.306
17DAP/reference	0.88003	0.195
27DAP/reference	1.3192	0.126
39DAP/reference	1.25717	0.346
41DAP/reference	1.18865	0.293
42DAP/reference	1.17515	0.18
43DAP/reference	0.80232	0.108
47DAP/reference	1.00538	0.749
52DAP/reference	0.88715	0.031
57DAP/reference	0.62899	0.018

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14658	0.588
17DAP/reference	1.24961	0.511
27DAP/reference	1.15466	0.1
39DAP/reference	1.11864	0.563
41DAP/reference	1.09022	0.439
42DAP/reference	1.35277	0.214
43DAP/reference	1.54989	0.082
47DAP/reference	0.93229	0.325
52DAP/reference	1.31435	0.077
57DAP/reference	2.52983	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96908	1
26DAP/20DAP	2.00818
34DAP/26DAP	0.85218	0.267
51DAP/34DAP	0.88321	0.428
52DAP/51DAP	0.80442
53DAP/52DAP	1.01766	1
55DAP/53DAP	0.87107	0.225
57DAP/55DAP	1.27836	0.898
62DAP/57DAP	N/A	N/A
68DAP/62DAP	2.14425	0.464
68DAP/14DAP	3.95786	0.019

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.4253	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.0794	0.417
Mature Green Tomato/Ripe Tomato	1.68109	0.119
Immature Eggplant/Mature Eggplant	1.07635	0.248
Ripe Pepper/Ripe Tomato	1.1128	1
Mature Eggplant/Ripe Tomato	1.11948	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01926	1
1-1-2/M82	0.95867	1
12-2/M82	0.82553	0.955
12-4/M82	0.96618	1
1-3/M82	2.39013	0.26
2-1-1/M82	0.9655	1
2-1/M82	0.87143	0.74
2-6/M82	1.02931	1
3-2/M82	1.00864
4-1-1/M82	1.50897	1
4-1/M82	1.61626	1
4-3-2/M82	1.47354	0.241
4-3/M82	1.34035	1
5-3/M82	1.18355	0.572
6-2/M82	0.98865	1
6-3/M82	0.70441	1
7-1/M82	1.07187	1
7-2/M82	0.97712	1
9-3-2/M82	1.402	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.30553
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	2.08163	1
IL12-4/WTpooled	0.73422	0.71
IL1-4/WTpooled	1.51692	1
WT/WTpooled	0.83341	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	1.25813	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07998	0.671
DC3000/delta hrp 6h	1.0365	0.95
DC3000/delta hrp 12h	1.04949	1
DC3000/delta hrp 24h	1.07421	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16452	0.29
DC3000 delta B/DC3000 delta AB	1.73388	0.093

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97129	1
Exp 36h	1.22438	1
Exp 60h	1.17536	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93005	1
Var 0h	1.34536	0.98
Var 12h I row2-row1	1.2093	0.736
Var 12h NI row2-row1	1.11631	1
Var 36h I row2-row1	1.19498	0.601
Var 36h NI row2-row1	0.7328	0.478
Var 60h I row2-row1	0.98367
Var 60h NI row2-row1	0.73011	0.292
Time course 0hI-0hNI	0.90477	0.256
Time course 12hI-12hNI	1.04549	0.724
Time course 36hI-36hNI	1.24635	0.218
Time course 60hI-60hNI	1.45356	0.015

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)	0.95139	0.614
transgenic ySAMdc/azygous control (breaker)	1.13724	1
transgenic ySAMdc/azygous control (red)	1.20308	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12334	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84576	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88801	1
Manapal/WT (break)	1.27438	0.14
Manapal/WT (red)	1.11847	1