Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.11.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96505	0.722
27DAP/17DAP	1.23814	0.801
39DAP/27DAP	0.79019	0.397
41DAP/39DAP	1.18605	0.504
42DAP/41DAP	0.93735	1
43DAP/42DAP	1.07958	1
47DAP/43DAP	1.14813	0.793
52DAP/47DAP	0.72657	0.339
57DAP/52DAP	1.12919	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7667	0.036
17DAP/reference	0.71577	0.011
27DAP/reference	0.70965	0.016
39DAP/reference	0.71422	0.043
41DAP/reference	0.80418	0.011
42DAP/reference	0.59416	0.001
43DAP/reference	0.7943	0.135
47DAP/reference	0.67504	0.001
52DAP/reference	0.7419	0.026
57DAP/reference	0.87026	0.056

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93025	0.47
27DAP/17DAP	1.01049	0.98
39DAP/27DAP	1.04449	0.663
41DAP/39DAP	1.08507	0.827
42DAP/41DAP	1.1078	0.539
43DAP/42DAP	0.92818	0.383
47DAP/43DAP	1.08411	0.331
52DAP/47DAP	1.04484	0.826
57DAP/52DAP	1.00113	1
57DAP/7DAP	0.99345	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76454	0.074
17DAP/reference	0.91281	0.253
27DAP/reference	0.91725	0.171
39DAP/reference	0.66154	0.011
41DAP/reference	0.59409	0.011
42DAP/reference	0.75604	0.053
43DAP/reference	0.92633	0.166
47DAP/reference	0.56509	0.05
52DAP/reference	0.81518	0.043
57DAP/reference	0.86036	0.132

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87512	0.197
17DAP/reference	0.57129	0.004
27DAP/reference	0.5869	0.035
39DAP/reference	0.50224	0.022
41DAP/reference	0.70698	0.083
42DAP/reference	0.6826	0.021
43DAP/reference	0.76987	0.144
47DAP/reference	0.86357	0.048
52DAP/reference	0.39994	0.003
57DAP/reference	0.52867	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82995	0.183
17DAP/reference	0.82202	0.249
27DAP/reference	0.82808	0.043
39DAP/reference	0.92886	0.36
41DAP/reference	0.90562	0.293
42DAP/reference	0.87175	0.287
43DAP/reference	0.8408	0.179
47DAP/reference	0.44249	0.004
52DAP/reference	0.79497	0.242
57DAP/reference	0.61402	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.11337	0.966
26DAP/20DAP	0.70767	0.205
34DAP/26DAP	1.13896	0.819
51DAP/34DAP	1.01655	0.898
52DAP/51DAP	0.88344	1
53DAP/52DAP	1.05358	0.845
55DAP/53DAP	1.07426	0.834
57DAP/55DAP	0.9809	0.88
62DAP/57DAP	1.13129	0.902
68DAP/62DAP	1.1329	0.897
68DAP/14DAP	0.81623	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.78016	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.19655	0.814
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.59947	0.293
Mature Eggplant/Ripe Tomato	0.61736	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.02444
12-2/M82	0.71582
12-4/M82	0.85829	1
1-3/M82	N/A	N/A
2-1-1/M82	0.86993	1
2-1/M82	N/A	N/A
2-6/M82	0.87804	1
3-2/M82	0.81809
4-1-1/M82	0.97189
4-1/M82	0.7795
4-3-2/M82	0.70537	0.698
4-3/M82	0.8785	1
5-3/M82	1.03667	1
6-2/M82	1.26609
6-3/M82	1.1826	1
7-1/M82	0.78898
7-2/M82	1.36853	1
9-3-2/M82	0.75387	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.08414	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08294	1
IL12-4/WTpooled	0.94362	0.71
IL1-4/WTpooled	0.94655	1
WT/WTpooled	0.98615	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	0.91182	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.21753	0.671
DC3000/delta hrp 6h	1.05672	0.95
DC3000/delta hrp 12h	0.96176
DC3000/delta hrp 24h	1.25138	0.336

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.2542	0.06
DC3000 delta B/DC3000 delta AB	0.8783	0.27

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	1.41937	0.693
Exp 60h	1.16071	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97207	1
Var 0h	0.92224	0.933
Var 12h I row2-row1	1.04322	0.692
Var 12h NI row2-row1	0.99961	1
Var 36h I row2-row1	1.1221	0.908
Var 36h NI row2-row1	0.83889	0.469
Var 60h I row2-row1	0.92274	0.285
Var 60h NI row2-row1	1.12946	0.904
Time course 0hI-0hNI	0.99008	0.985
Time course 12hI-12hNI	1.08525	0.175
Time course 36hI-36hNI	1.18799	0.007
Time course 60hI-60hNI	1.47714	0.017

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)	1.20156	0.3
transgenic ySAMdc/azygous control (breaker)	1.57747	0.162
transgenic ySAMdc/azygous control (red)	0.97961	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00522	0.687

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98006	1
Manapal/WT (break)	0.8598	0.299
Manapal/WT (red)	0.79607	0.181