Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.20.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06958	0.827
27DAP/17DAP	1.16094	0.847
39DAP/27DAP	0.74684	0.364
41DAP/39DAP	1.38178	0.691
42DAP/41DAP	1.10438	0.852
43DAP/42DAP	1.0206	1
47DAP/43DAP	1.14619	0.825
52DAP/47DAP	1.0076	0.906
57DAP/52DAP	1.35594	0.758

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88544	0.136
17DAP/reference	0.99663	0.904
27DAP/reference	1.00587	0.923
39DAP/reference	0.8805	0.081
41DAP/reference	0.88943	0.154
42DAP/reference	0.79478	0.001
43DAP/reference	0.86243	0.071
47DAP/reference	0.86716	0.016
52DAP/reference	0.84391	0.091
57DAP/reference	0.94887	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.7954	0.201
27DAP/17DAP	1.13665	0.645
39DAP/27DAP	1.00566	0.984
41DAP/39DAP	0.96408	0.986
42DAP/41DAP	0.81285	0.078
43DAP/42DAP	1.01383	1
47DAP/43DAP	1.21144	0.735
52DAP/47DAP	1.28198	0.334
57DAP/52DAP	1.04697	0.971
57DAP/7DAP	0.73481	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93311	0.138
17DAP/reference	1.09715	0.525
27DAP/reference	0.96893	0.462
39DAP/reference	1.10706	0.062
41DAP/reference	0.9785	0.512
42DAP/reference	1.08384	0.308
43DAP/reference	1.1598	0.325
47DAP/reference	1.03319	1
52DAP/reference	1.16688	0.13
57DAP/reference	1.04625	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77612	0.076
17DAP/reference	0.78611	0.014
27DAP/reference	0.80133	0.044
39DAP/reference	0.91494	0.14
41DAP/reference	0.8565	0.089
42DAP/reference	0.86053	0.098
43DAP/reference	0.86679	0.236
47DAP/reference	0.89052	0.042
52DAP/reference	0.98009	0.5
57DAP/reference	1.04076	0.93

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14929	0.218
17DAP/reference	0.97597	0.668
27DAP/reference	1.12468	0.216
39DAP/reference	1.08144	0.353
41DAP/reference	1.22631	0.125
42DAP/reference	1.03414	0.979
43DAP/reference	1.00333	0.796
47DAP/reference	0.89678	0.168
52DAP/reference	1.09163	0.735
57DAP/reference	0.93531	0.315

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17397	0.966
26DAP/20DAP	1.30722	0.594
34DAP/26DAP	1.14569	0.819
51DAP/34DAP	1.16272	0.224
52DAP/51DAP	0.95686	1
53DAP/52DAP	1.20063	0.868
55DAP/53DAP	0.95932	0.82
57DAP/55DAP	0.97225	0.845
62DAP/57DAP	0.89672	0.681
68DAP/62DAP	1.18661	1
68DAP/14DAP	1.1936	0.578

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15237	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.06955	0.948
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.86677
Mature Eggplant/Ripe Tomato	N/A	N/A

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	0.90745
1-3/M82	N/A	N/A
2-1-1/M82	0.84868
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	1.04575	1
6-2/M82	0.63631
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.95048
9-3-2/M82	0.7861

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	0.69184

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94031	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.99805	1
DC3000/delta hrp 24h	0.94058	0.564

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	0.98644	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.19105	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.95928	0.565
Var 12h NI row2-row1	1.65207	0.649
Var 36h I row2-row1	1.35182	1
Var 36h NI row2-row1	1.28293
Var 60h I row2-row1	1.03442	1
Var 60h NI row2-row1	0.53585	1
Time course 0hI-0hNI	1.04988	0.662
Time course 12hI-12hNI	1.34729	0.621
Time course 36hI-36hNI	2.53025	0.063
Time course 60hI-60hNI	1.93414	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)	1.10341	0.372
transgenic ySAMdc/azygous control (breaker)	1.01735	1
transgenic ySAMdc/azygous control (red)	0.97567	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9999	0.967

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16262	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81126	1
Manapal/WT (break)	0.88974	1
Manapal/WT (red)	0.91095	0.216