Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.10.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03008	0.947
27DAP/17DAP	1.04463	0.892
39DAP/27DAP	0.80124	0.474
41DAP/39DAP	1.18991	0.26
42DAP/41DAP	0.93513	1
43DAP/42DAP	1.02083	0.948
47DAP/43DAP	1.10081	0.584
52DAP/47DAP	0.95965	0.816
57DAP/52DAP	1.01056	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99708	0.756
17DAP/reference	0.9991	1
27DAP/reference	1.0162	0.599
39DAP/reference	1.00634	0.903
41DAP/reference	1.03469	0.287
42DAP/reference	0.97529	0.259
43DAP/reference	1.03849	0.471
47DAP/reference	1.00737	1
52DAP/reference	0.95878	0.438
57DAP/reference	1.11973	0.127

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90806	0.323
27DAP/17DAP	1.00134	1
39DAP/27DAP	1.02448	0.77
41DAP/39DAP	1.01994	0.853
42DAP/41DAP	0.95177	0.69
43DAP/42DAP	1.04476	0.297
47DAP/43DAP	1.00481	0.973
52DAP/47DAP	0.98316	0.941
57DAP/52DAP	0.96276	0.605
57DAP/7DAP	1.07722	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86668	0.129
17DAP/reference	0.85667	0.011
27DAP/reference	0.8365	0.01
39DAP/reference	0.83532	0.011
41DAP/reference	0.9316	0.166
42DAP/reference	0.77139	0.012
43DAP/reference	0.78946	0.012
47DAP/reference	0.85427	0.057
52DAP/reference	0.82606	0.011
57DAP/reference	0.80816	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98565	0.736
17DAP/reference	0.94942	0.201
27DAP/reference	0.85594	0.097
39DAP/reference	0.89952	0.083
41DAP/reference	0.9417	0.268
42DAP/reference	0.96091	0.355
43DAP/reference	0.95832	0.45
47DAP/reference	0.99055	0.559
52DAP/reference	0.92107	0.121
57DAP/reference	0.92849	0.079

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81082	0.028
17DAP/reference	0.91314	0.224
27DAP/reference	0.89171	0.049
39DAP/reference	0.86461	0.009
41DAP/reference	0.83921	0.021
42DAP/reference	0.79652	0.014
43DAP/reference	0.84315	0.029
47DAP/reference	0.93827	0.161
52DAP/reference	0.87822	0.169
57DAP/reference	0.82926	0.039

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00054	1
26DAP/20DAP	0.99828	1
34DAP/26DAP	1.00467	1
51DAP/34DAP	1.03815	0.84
52DAP/51DAP	0.99715	1
53DAP/52DAP	N/A	N/A
55DAP/53DAP	0.87168
57DAP/55DAP	1.04128	0.935
62DAP/57DAP	0.96072	0.994
68DAP/62DAP	1.15063	0.182
68DAP/14DAP	1.23468	0.487

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04079	0.391

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.74837
Mature Green Tomato/Ripe Tomato	0.88965	0.377
Immature Eggplant/Mature Eggplant	0.81096	0.545
Ripe Pepper/Ripe Tomato	0.68932	1
Mature Eggplant/Ripe Tomato	0.72476	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.93658	0.736
1-1-2/M82	0.99941	1
12-2/M82	0.95527	0.955
12-4/M82	1.02252	1
1-3/M82	1.00558	1
2-1-1/M82	0.98297	1
2-1/M82	1.01063	1
2-6/M82	0.98704	1
3-2/M82	1.07864
4-1-1/M82	1.01803	1
4-1/M82	0.90957
4-3-2/M82	1.37054
4-3/M82	0.92232	0.72
5-3/M82	1.04313	1
6-2/M82	1.02772	1
6-3/M82	0.97518	1
7-1/M82	1.05873	0.598
7-2/M82	0.92885	0.881
9-3-2/M82	0.71528

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	0.82014
IL1-4/WTpooled	3.61341	1
WT/WTpooled	1.01964

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	1.26585	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95741
DC3000/delta hrp 6h	1.25568	1
DC3000/delta hrp 12h	1.01931
DC3000/delta hrp 24h	0.98985	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00132	1
DC3000 delta B/DC3000 delta AB	1.0572	0.462

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	1.34204	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97868	1
Var 0h	1.01758	1
Var 12h I row2-row1	1.1592	0.224
Var 12h NI row2-row1	0.92625	0.546
Var 36h I row2-row1	0.93876	1
Var 36h NI row2-row1	1.02679	1
Var 60h I row2-row1	1.1362	1
Var 60h NI row2-row1	1.08932	0.904
Time course 0hI-0hNI	1.04296	0.852
Time course 12hI-12hNI	1.01328	0.849
Time course 36hI-36hNI	0.98922	0.621
Time course 60hI-60hNI	1.08131	0.137

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)	1.01124	1
transgenic ySAMdc/azygous control (breaker)	1.26021	0.248
transgenic ySAMdc/azygous control (red)	1.1983	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96885	0.115

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.939	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86519	1
Manapal/WT (break)	0.8698	1
Manapal/WT (red)	0.78293	0.181