Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.1.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.8857	0.464
27DAP/17DAP	0.81326	0.49
39DAP/27DAP	0.66392	0.382
41DAP/39DAP	0.67344	0.101
42DAP/41DAP	0.81025	0.774
43DAP/42DAP	1.12479	0.809
47DAP/43DAP	1.08952	0.876
52DAP/47DAP	1.06155	0.946
57DAP/52DAP	1.60415	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96984	0.55
17DAP/reference	0.84216	0.208
27DAP/reference	1.05992	0.648
39DAP/reference	0.76301	0.09
41DAP/reference	0.82025	0.267
42DAP/reference	0.82365	0.014
43DAP/reference	0.77743	N/A
47DAP/reference	0.76453	0.001
52DAP/reference	0.918	0.3
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.55275	0.041
27DAP/17DAP	0.78339	0.158
39DAP/27DAP	0.55672	0.029
41DAP/39DAP	1.27328	0.719
42DAP/41DAP	0.97136	0.764
43DAP/42DAP	0.46758	0.022
47DAP/43DAP	0.86157	0.499
52DAP/47DAP	0.6759	0.329
57DAP/52DAP	0.66973	0.103
57DAP/7DAP	0.69128	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.35502	0.032
17DAP/reference	1.22118	0.035
27DAP/reference	0.86453	0.062
39DAP/reference	1.25717	0.022
41DAP/reference	0.88354	0.235
42DAP/reference	0.92845	0.151
43DAP/reference	0.96369	0.368
47DAP/reference	0.89573	0.222
52DAP/reference	0.99362	0.621
57DAP/reference	1.09457	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01105	0.933
17DAP/reference	0.70347	0.012
27DAP/reference	0.88704	0.203
39DAP/reference	0.99031	0.539
41DAP/reference	0.92065	0.188
42DAP/reference	0.9406	0.392
43DAP/reference	0.84628	0.135
47DAP/reference	0.80856	0.013
52DAP/reference	0.75448	0.018
57DAP/reference	0.78064	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.81245	0.018
17DAP/reference	1.15678	0.294
27DAP/reference	1.50829	0.056
39DAP/reference	1.15222	0.094
41DAP/reference	1.04945	0.818
42DAP/reference	4.65881	0.014
43DAP/reference	2.2983	0.109
47DAP/reference	0.85909	0.207
52DAP/reference	3.04787	0.07
57DAP/reference	1.08435	0.452

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97139	1
26DAP/20DAP	1.15915	0.562
34DAP/26DAP	0.77833	0.381
51DAP/34DAP	1.14017	0.261
52DAP/51DAP	1.08332	0.77
53DAP/52DAP	0.69822	0.079
55DAP/53DAP	0.70557	0.336
57DAP/55DAP	0.71386	0.433
62DAP/57DAP	0.81359	N/A
68DAP/62DAP	0.86791	0.747
68DAP/14DAP	1.06713	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.32982	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.01471	0.726
Mature Green Tomato/Ripe Tomato	16.6918	0.015
Immature Eggplant/Mature Eggplant	0.28198	0.062
Ripe Pepper/Ripe Tomato	10.4563	1
Mature Eggplant/Ripe Tomato	5.15285	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	0.63137	0.358
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	0.95668	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	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.41005	0.362
IL12-4/WTpooled	0.95169	1
IL1-4/WTpooled	1.05164	1
WT/WTpooled	0.95655	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	1.00323	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87444	1
DC3000/delta hrp 6h	0.89725	0.95
DC3000/delta hrp 12h	1.15847	1
DC3000/delta hrp 24h	0.53397	0.038

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.52158	0.025
DC3000 delta B/DC3000 delta AB	0.4969	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.89457	1
Exp 36h	0.7598	0.406
Exp 60h	0.8561	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00186	1
Var 0h	1.07127	0.98
Var 12h I row2-row1	1.02863	0.795
Var 12h NI row2-row1	1.40402	0.281
Var 36h I row2-row1	1.22695	0.298
Var 36h NI row2-row1	0.94157	0.706
Var 60h I row2-row1	1.08921	1
Var 60h NI row2-row1	0.73016	0.431
Time course 0hI-0hNI	1.20575	0.227
Time course 12hI-12hNI	1.01997	1
Time course 36hI-36hNI	1.58827	0.006
Time course 60hI-60hNI	2.1921	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)	1.08105	0.455
transgenic ySAMdc/azygous control (breaker)	2.0147	0.172
transgenic ySAMdc/azygous control (red)	1.16391	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99627	0.832

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.13756	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.43087	0.083
Manapal/WT (break)	4.87377	0.123
Manapal/WT (red)	8.6305	0.137