Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.7.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.51139	0.198
27DAP/17DAP	0.56696	0.049
39DAP/27DAP	0.68701	0.326
41DAP/39DAP	0.66326	0.087
42DAP/41DAP	0.70407	0.397
43DAP/42DAP	1.13967	0.899
47DAP/43DAP	0.47282	0.049
52DAP/47DAP	1.09897	0.934
57DAP/52DAP	1.31164	0.963

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88044	0.238
17DAP/reference	0.61619	0.014
27DAP/reference	0.82407	0.17
39DAP/reference	0.67399	0.042
41DAP/reference	0.58093	0.021
42DAP/reference	0.86428	0.043
43DAP/reference	0.87866	0.234
47DAP/reference	0.83391	0.055
52DAP/reference	0.93657	0.341
57DAP/reference	1.32634	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47264	0.051
27DAP/17DAP	0.80085	0.312
39DAP/27DAP	0.55953	0.058
41DAP/39DAP	1.1535	0.362
42DAP/41DAP	0.86714	0.122
43DAP/42DAP	0.88708	0.132
47DAP/43DAP	1.06562	0.69
52DAP/47DAP	1.04229	0.851
57DAP/52DAP	1.30318	0.206
57DAP/7DAP	0.74131	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.37311	0.052
17DAP/reference	1.07406	0.18
27DAP/reference	0.97137	0.494
39DAP/reference	0.81449	0.034
41DAP/reference	0.8607	0.067
42DAP/reference	0.89483	0.211
43DAP/reference	0.65741	0.014
47DAP/reference	0.85025	0.222
52DAP/reference	0.91088	0.232
57DAP/reference	0.7121	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.64896	0.019
17DAP/reference	0.61631	0.009
27DAP/reference	0.85533	0.167
39DAP/reference	0.86561	0.235
41DAP/reference	0.96817	0.384
42DAP/reference	0.97233	0.392
43DAP/reference	0.4581	0.005
47DAP/reference	0.83358	0.06
52DAP/reference	0.59622	0.003
57DAP/reference	0.36017	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.10206	0.031
17DAP/reference	1.88156	0.217
27DAP/reference	1.54161	0.035
39DAP/reference	1.47399	0.022
41DAP/reference	1.15938	0.074
42DAP/reference	1.11591	0.529
43DAP/reference	1.16866	0.755
47DAP/reference	0.83159	0.161
52DAP/reference	0.63774	0.047
57DAP/reference	2.18446	0.011

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05787	0.966
26DAP/20DAP	1.05791	1
34DAP/26DAP	0.84197	0.387
51DAP/34DAP	0.67954	0.064
52DAP/51DAP	1.01649	0.821
53DAP/52DAP	0.91502	0.498
55DAP/53DAP	0.92974	0.675
57DAP/55DAP	0.87679	0.539
62DAP/57DAP	0.98523	0.994
68DAP/62DAP	3.12222	0.03
68DAP/14DAP	3.5856	0.018

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.74911	0.023

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.84256	0.063
Mature Green Tomato/Ripe Tomato	9.7238	0.015
Immature Eggplant/Mature Eggplant	0.55719	0.062
Ripe Pepper/Ripe Tomato	2.25593	0.256
Mature Eggplant/Ripe Tomato	8.70178	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.11112	0.365
IL2-6/WTpooled	0.99568	1
IL7-5/WTpooled	1.09066	0.792
IL7-3/WTpooled	1.05487	1
IL12-4/WTpooled	0.96806	1
IL1-4/WTpooled	1.11436	1
WT/WTpooled	1.00312	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	1.10808	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89623	1
DC3000/delta hrp 6h	0.99296	0.95
DC3000/delta hrp 12h	0.9302	1
DC3000/delta hrp 24h	0.63541	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88864	0.388
DC3000 delta B/DC3000 delta AB	0.65001	0.036

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	0.99586	1
Var 0h	0.97382	1
Var 12h I row2-row1	0.9254	0.514
Var 12h NI row2-row1	1.0001	1
Var 36h I row2-row1	0.78774	0.805
Var 36h NI row2-row1	0.94783	0.743
Var 60h I row2-row1	1.10331	0.562
Var 60h NI row2-row1	0.98737	1
Time course 0hI-0hNI	1.04611	0.451
Time course 12hI-12hNI	1.02125	0.803
Time course 36hI-36hNI	1.0678	0.128
Time course 60hI-60hNI	1.03675	0.673

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)	1.02624	1
transgenic ySAMdc/azygous control (breaker)	1.76383	0.161
transgenic ySAMdc/azygous control (red)	1.05038	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.58118	0.078

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.69298	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	15.8774	0.083
Manapal/WT (break)	5.58655	0.123
Manapal/WT (red)	1.53215	0.222