Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.14.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70647	0.054
27DAP/17DAP	0.79448	0.478
39DAP/27DAP	1.25854	0.372
41DAP/39DAP	0.55873	0.047
42DAP/41DAP	0.765	0.774
43DAP/42DAP	0.90094	0.801
47DAP/43DAP	0.66527	0.16
52DAP/47DAP	1.13582	0.906
57DAP/52DAP	1.18767	0.955

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.6973	0.043
17DAP/reference	0.84786	0.342
27DAP/reference	0.67999	0.057
39DAP/reference	0.70891	0.149
41DAP/reference	0.6994	0.031
42DAP/reference	1.05726	0.137
43DAP/reference	0.75227	0.058
47DAP/reference	0.89077	0.046
52DAP/reference	0.69605	0.105
57DAP/reference	0.72674	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88952	0.245
27DAP/17DAP	0.98689	0.887
39DAP/27DAP	0.7926	0.061
41DAP/39DAP	1.25324	0.909
42DAP/41DAP	0.94201	0.568
43DAP/42DAP	0.82253	0.043
47DAP/43DAP	0.97047	0.855
52DAP/47DAP	0.55855	0.041
57DAP/52DAP	0.81684	0.221
57DAP/7DAP	0.30796	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.0869	0.024
17DAP/reference	2.3278	0.006
27DAP/reference	1.51722	0.014
39DAP/reference	1.28347	0.017
41DAP/reference	1.53661	0.011
42DAP/reference	1.34853	0.076
43DAP/reference	1.24746	0.132
47DAP/reference	1.12981	0.395
52DAP/reference	1.14228	0.401
57DAP/reference	1.01676	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21712	0.531
17DAP/reference	1.46131	0.021
27DAP/reference	1.4756	0.071
39DAP/reference	0.91309	0.168
41DAP/reference	1.17166	0.188
42DAP/reference	1.35626	0.051
43DAP/reference	0.86482	0.25
47DAP/reference	0.99157	0.609
52DAP/reference	0.56563	0.003
57DAP/reference	0.59995	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.24811	0.017
17DAP/reference	1.44067	0.248
27DAP/reference	1.53708	0.022
39DAP/reference	1.59519	0.008
41DAP/reference	1.13304	0.286
42DAP/reference	1.0491	0.848
43DAP/reference	1.19689	0.237
47DAP/reference	0.46788	0.004
52DAP/reference	0.99945	0.871
57DAP/reference	0.90477	0.293

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01714	1
26DAP/20DAP	4.65487	0.097
34DAP/26DAP	0.76901	0.394
51DAP/34DAP	0.9257	0.522
52DAP/51DAP	0.81438	0.151
53DAP/52DAP	0.86413	0.374
55DAP/53DAP	0.75601	0.064
57DAP/55DAP	1.19562	0.986
62DAP/57DAP	0.96501	0.994
68DAP/62DAP	1.03381	0.885
68DAP/14DAP	1.10255	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.94791	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79909	0.251
Mature Green Tomato/Ripe Tomato	1.94602	0.022
Immature Eggplant/Mature Eggplant	1.1506	0.101
Ripe Pepper/Ripe Tomato	1.36775	0.258
Mature Eggplant/Ripe Tomato	1.77978	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94122	0.944
1-1-2/M82	1.23242	1
12-2/M82	0.78465	0.862
12-4/M82	1.02064	1
1-3/M82	1.71075	0.26
2-1-1/M82	0.86181	0.683
2-1/M82	1.19973	1
2-6/M82	1.23238	0.594
3-2/M82	1.1548
4-1-1/M82	1.50716	1
4-1/M82	2.14896
4-3-2/M82	2.4729	0.232
4-3/M82	1.7504	0.268
5-3/M82	1.2206	0.572
6-2/M82	2.62537
6-3/M82	1.01533	1
7-1/M82	1.22372	0.925
7-2/M82	1.74488	0.291
9-3-2/M82	2.04621

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94942	0.321
IL2-6/WTpooled	0.96911	1
IL7-5/WTpooled	1.12019	1
IL7-3/WTpooled	1.01114	1
IL12-4/WTpooled	0.94011	0.71
IL1-4/WTpooled	0.9637	0.562
WT/WTpooled	0.96023	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	0.97185	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98587	1
DC3000/delta hrp 6h	0.9454	0.95
DC3000/delta hrp 12h	1.16247	1
DC3000/delta hrp 24h	1.14013	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.59388	0.043
DC3000 delta B/DC3000 delta AB	1.55739	0.105

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.2579	1
Exp 36h	1.11703	1
Exp 60h	1.6076	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99448	1
Var 0h	1.28115	0.421
Var 12h I row2-row1	1.01666	1
Var 12h NI row2-row1	1.16867	0.649
Var 36h I row2-row1	1.22788	0.309
Var 36h NI row2-row1	0.88609	0.61
Var 60h I row2-row1	0.86047	0.285
Var 60h NI row2-row1	0.81869	0.516
Time course 0hI-0hNI	1.09635	0.537
Time course 12hI-12hNI	1.0247	0.811
Time course 36hI-36hNI	1.53066	0.005
Time course 60hI-60hNI	2.7634	0.009

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)	1.06959	0.511
transgenic ySAMdc/azygous control (breaker)	1.06806	1
transgenic ySAMdc/azygous control (red)	1.15124	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.45095	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.64643	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.01012	1
Manapal/WT (break)	1.12025	0.381
Manapal/WT (red)	0.86985	0.188