Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.13.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.65613	0.134
27DAP/17DAP	2.22066	0.131
39DAP/27DAP	1.01095	0.857
41DAP/39DAP	0.61205	0.147
42DAP/41DAP	1.18753	0.626
43DAP/42DAP	0.92287	0.775
47DAP/43DAP	0.83425	0.496
52DAP/47DAP	3.31254	0.044
57DAP/52DAP	0.54248	0.507

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13134	0.334
17DAP/reference	0.87546	0.129
27DAP/reference	0.91057	0.249
39DAP/reference	0.83569	0.031
41DAP/reference	0.79122	0.026
42DAP/reference	1.29049	0.001
43DAP/reference	0.97568	0.594
47DAP/reference	1.0954	0.329
52DAP/reference	1.01612	1
57DAP/reference	0.98922	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85117	0.388
27DAP/17DAP	0.93617	0.684
39DAP/27DAP	1.25047	0.231
41DAP/39DAP	2.07936	0.018
42DAP/41DAP	0.71801	0.021
43DAP/42DAP	1.39839	0.014
47DAP/43DAP	1.19756	0.039
52DAP/47DAP	1.35984	0.255
57DAP/52DAP	2.0678	0.033
57DAP/7DAP	2.11458

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74154	0.08
17DAP/reference	0.99359	0.599
27DAP/reference	0.94005	0.303
39DAP/reference	0.78667	0.021
41DAP/reference	0.83312	0.039
42DAP/reference	1.22889	0.686
43DAP/reference	1.38541	0.031
47DAP/reference	0.78175	0.222
52DAP/reference	1.31016	0.021
57DAP/reference	1.25499	0.076

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97528	0.669
17DAP/reference	1.00956	0.851
27DAP/reference	1.02273	1
39DAP/reference	1.00657	1
41DAP/reference	1.1473	0.129
42DAP/reference	1.13429	0.369
43DAP/reference	1.08905	0.417
47DAP/reference	0.98402	0.559
52DAP/reference	0.78261	0.018
57DAP/reference	1.1285	0.437

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93486	0.158
17DAP/reference	0.90477	0.189
27DAP/reference	0.99054	0.691
39DAP/reference	1.08875	0.1
41DAP/reference	0.9369	0.417
42DAP/reference	1.03114	1
43DAP/reference	1.35595	0.011
47DAP/reference	1.26416	0.093
52DAP/reference	2.0597	0.094
57DAP/reference	1.28319	0.153

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12314	1
26DAP/20DAP	0.64815	0.228
34DAP/26DAP	1.39642	0.819
51DAP/34DAP	0.94513	0.722
52DAP/51DAP	1.23464	0.367
53DAP/52DAP	0.78799	0.1
55DAP/53DAP	1.13773	0.696
57DAP/55DAP	1.09796	0.348
62DAP/57DAP	1.34581	0.217
68DAP/62DAP	0.87076	0.609
68DAP/14DAP	0.58975	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01532	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.08105	0.018
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.06182	0.224
Mature Eggplant/Ripe Tomato	0.13507	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.77718
12-2/M82	N/A	N/A
12-4/M82	1.19759	1
1-3/M82	0.71591
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	2.5783	0.594
3-2/M82	0.79414	0.752
4-1-1/M82	N/A	N/A
4-1/M82	2.4297
4-3-2/M82	N/A	N/A
4-3/M82	2.15148	1
5-3/M82	0.58812	0.49
6-2/M82	2.11034
6-3/M82	1.16096	1
7-1/M82	0.49763
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	N/A	N/A
IL2-6/WTpooled	0.98528	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95277	1
IL12-4/WTpooled	0.99061	1
IL1-4/WTpooled	1.12876
WT/WTpooled	1.01215	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	3.01137	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.20034	0.823
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.18132	1
DC3000/delta hrp 24h	0.84212	0.252

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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	1.08199	1
Var 0h	0.68444	1
Var 12h I row2-row1	0.99899	1
Var 12h NI row2-row1	0.60091	0.906
Var 36h I row2-row1	0.83738	0.805
Var 36h NI row2-row1	0.64923	0.61
Var 60h I row2-row1	0.8738	0.293
Var 60h NI row2-row1	0.8775	1
Time course 0hI-0hNI	0.99204	0.947
Time course 12hI-12hNI	1.50509	0.216
Time course 36hI-36hNI	10.4691	0.005
Time course 60hI-60hNI	7.17199	0.008

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)	1.7685	0.289
transgenic ySAMdc/azygous control (breaker)	0.27528	0.122
transgenic ySAMdc/azygous control (red)	1.40184	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95323	0.214

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.12651	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75153	1
Manapal/WT (break)	0.50781	0.333
Manapal/WT (red)	0.2732	0.181