Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.1.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98362	0.83
27DAP/17DAP	0.87166	0.637
39DAP/27DAP	1.75075	0.113
41DAP/39DAP	1.07343	0.63
42DAP/41DAP	1.10951	0.868
43DAP/42DAP	0.85434	0.773
47DAP/43DAP	0.90922	0.667
52DAP/47DAP	1.13896	0.811
57DAP/52DAP	1.07565	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.34701	0.081
17DAP/reference	0.92414	0.368
27DAP/reference	1.7383	0.009
39DAP/reference	1.22201	0.122
41DAP/reference	1.00424	1
42DAP/reference	1.28207	0.003
43DAP/reference	0.81505	0.024
47DAP/reference	1.07183	0.91
52DAP/reference	0.96196	0.427
57DAP/reference	1.13532	0.136

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95628	0.595
27DAP/17DAP	1.00704	1
39DAP/27DAP	1.04009	0.672
41DAP/39DAP	0.86365	0.347
42DAP/41DAP	1.00339	0.929
43DAP/42DAP	1.00812	0.788
47DAP/43DAP	0.96294	0.666
52DAP/47DAP	0.96745	0.848
57DAP/52DAP	0.94031	0.532
57DAP/7DAP	1.00628	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89531	0.203
17DAP/reference	0.93773	0.253
27DAP/reference	0.86531	0.01
39DAP/reference	0.86833	0.011
41DAP/reference	0.84116	0.026
42DAP/reference	0.87984	0.07
43DAP/reference	0.87735	0.04
47DAP/reference	1.54028	0.161
52DAP/reference	0.82161	0.028
57DAP/reference	0.82763	0.039

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09297	0.319
17DAP/reference	1.00557	0.747
27DAP/reference	1.59878	0.041
39DAP/reference	1.56777	0.023
41DAP/reference	1.49993	0.012
42DAP/reference	1.33287	0.017
43DAP/reference	1.44854	0.117
47DAP/reference	1.44709	0.011
52DAP/reference	0.92372	0.121
57DAP/reference	1.39637	0.055

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89075	0.098
17DAP/reference	0.90334	0.189
27DAP/reference	0.79534	0.025
39DAP/reference	0.91427	0.246
41DAP/reference	0.93913	0.331
42DAP/reference	0.86127	0.108
43DAP/reference	0.87389	0.137
47DAP/reference	0.73707	0.022
52DAP/reference	1.0001	0.8
57DAP/reference	1.423	0.085

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.21513	0.966
26DAP/20DAP	0.94828	0.317
34DAP/26DAP	1.19865	0.819
51DAP/34DAP	1.30941	0.054
52DAP/51DAP	0.83405	0.07
53DAP/52DAP	1.29072	0.144
55DAP/53DAP	0.99914	0.939
57DAP/55DAP	0.8789	0.443
62DAP/57DAP	1.11746	0.868
68DAP/62DAP	0.95679	0.885
68DAP/14DAP	1.21036	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.41153	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.42274	0.058
Mature Green Tomato/Ripe Tomato	1.70313	0.437
Immature Eggplant/Mature Eggplant	1.24326	0.055
Ripe Pepper/Ripe Tomato	0.54887	1
Mature Eggplant/Ripe Tomato	0.8454	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.34666
1-1-2/M82	0.65312
12-2/M82	N/A	N/A
12-4/M82	0.91778	1
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	0.98873
4-3/M82	1.19995
5-3/M82	1.87877	0.455
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	1.04473	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.10594	0.365
IL2-6/WTpooled	1.05219	0.659
IL7-5/WTpooled	1.00869	1
IL7-3/WTpooled	0.96032	1
IL12-4/WTpooled	0.90598	0.581
IL1-4/WTpooled	1.09647	0.399
WT/WTpooled	0.83997	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	1.03351	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06848	0.914
DC3000/delta hrp 6h	1.07156	1
DC3000/delta hrp 12h	1.03564	1
DC3000/delta hrp 24h	0.79646	0.092

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04101	0.11
DC3000 delta B/DC3000 delta AB	1.06159	0.479

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2638	1
Exp 36h	1.41533	0.693
Exp 60h	1.48884	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9989	1
Var 0h	0.46849	0.933
Var 12h I row2-row1	1.10819	0.654
Var 12h NI row2-row1	1.02199	1
Var 36h I row2-row1	1.01888	1
Var 36h NI row2-row1	1.02352	1
Var 60h I row2-row1	0.92951	0.306
Var 60h NI row2-row1	0.96126	1
Time course 0hI-0hNI	0.94343	0.634
Time course 12hI-12hNI	0.98946	0.956
Time course 36hI-36hNI	0.94809	0.418
Time course 60hI-60hNI	0.81886	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)	0.82157	0.246
transgenic ySAMdc/azygous control (breaker)	0.86763	0.49
transgenic ySAMdc/azygous control (red)	1.04754	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12635	0.086

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.52446	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81633	1
Manapal/WT (break)	1.7793	0.381
Manapal/WT (red)	0.64459	0.36