Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.4.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15777	0.876
27DAP/17DAP	1.69444	0.366
39DAP/27DAP	1.77409	0.109
41DAP/39DAP	0.88386	0.518
42DAP/41DAP	1.04225	1
43DAP/42DAP	0.95309	0.874
47DAP/43DAP	1.04908	0.965
52DAP/47DAP	1.67907	0.152
57DAP/52DAP	1.33532	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7845	0.118
17DAP/reference	0.42907	0.007
27DAP/reference	0.61322	0.043
39DAP/reference	0.30178	0.02
41DAP/reference	0.37455	0.009
42DAP/reference	2.11785	0.001
43DAP/reference	0.77151
47DAP/reference	1.15229	0.065
52DAP/reference	0.62903	0.082
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20977	0.043
27DAP/17DAP	0.94878	0.782
39DAP/27DAP	1.48757	0.057
41DAP/39DAP	1.72763	0.061
42DAP/41DAP	0.64054	0.011
43DAP/42DAP	1.41255	0.014
47DAP/43DAP	1.00631	0.973
52DAP/47DAP	1.44818	0.151
57DAP/52DAP	1.33067	0.169
57DAP/7DAP	2.12021	0.23

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2092	0.209
17DAP/reference	1.16297	0.244
27DAP/reference	1.82816	0.007
39DAP/reference	1.39511	0.03
41DAP/reference	1.93855	0.011
42DAP/reference	3.01471	0.007
43DAP/reference	3.38969	0.006
47DAP/reference	2.24113	0.018
52DAP/reference	2.2121	0.007
57DAP/reference	2.93661	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.52804	0.056
17DAP/reference	0.81176	0.159
27DAP/reference	1.07435	1
39DAP/reference	1.00549	0.569
41DAP/reference	1.22829	0.062
42DAP/reference	1.51222	0.024
43DAP/reference	1.26099	0.835
47DAP/reference	2.60583	0.011
52DAP/reference	0.59111	0.004
57DAP/reference	1.0973	0.72

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90772	0.23
17DAP/reference	0.69614	0.198
27DAP/reference	1.31013	0.044
39DAP/reference	1.17122	0.227
41DAP/reference	0.96898	0.512
42DAP/reference	1.18256	0.233
43DAP/reference	1.45729	0.052
47DAP/reference	1.26747	0.251
52DAP/reference	1.57398	0.035
57DAP/reference	2.71944	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10454	1
26DAP/20DAP	0.80381	0.113
34DAP/26DAP	0.91457	0.548
51DAP/34DAP	0.64051	0.081
52DAP/51DAP	0.89524	1
53DAP/52DAP	1.36876	0.057
55DAP/53DAP	1.04174	0.948
57DAP/55DAP	0.90968	0.623
62DAP/57DAP	0.90803	0.681
68DAP/62DAP	1.04287	0.944
68DAP/14DAP	1.09838	0.889

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	15.8105	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.33525	0.088
Mature Green Tomato/Ripe Tomato	0.28987	0.016
Immature Eggplant/Mature Eggplant	6.76314	0.05
Ripe Pepper/Ripe Tomato	0.13306	0.224
Mature Eggplant/Ripe Tomato	0.12535	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.75696
1-1-2/M82	1.03109	1
12-2/M82	1.11383	1
12-4/M82	1.31579	0.694
1-3/M82	6.46201	0.248
2-1-1/M82	1.46047	0.422
2-1/M82	0.96232
2-6/M82	1.54055	0.505
3-2/M82	N/A	N/A
4-1-1/M82	2.48422	0.876
4-1/M82	N/A	N/A
4-3-2/M82	2.21577	0.253
4-3/M82	1.50548	0.268
5-3/M82	0.91705	1
6-2/M82	3.22809	0.222
6-3/M82	1.57532	1
7-1/M82	1.44781
7-2/M82	2.89461	0.385
9-3-2/M82	1.20704	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.15367
IL2-6/WTpooled	0.55719
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.81026
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.38484

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	1.55547	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.16512	0.692
DC3000/delta hrp 6h	1.16625	0.978
DC3000/delta hrp 12h	1.03122	1
DC3000/delta hrp 24h	1.87465	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.19183	0.042
DC3000 delta B/DC3000 delta AB	5.29644

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.34508	1
Exp 36h	1.98507	0.489
Exp 60h	1.58674	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	0.67981
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.9889	0.789
transgenic ySAMdc/azygous control (breaker)	0.62263	0.132
transgenic ySAMdc/azygous control (red)	1.0436	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	2.02225	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88447	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.75568	1
Manapal/WT (break)	0.76875	1
Manapal/WT (red)	1.26647	0.413