Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.9.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15879	0.615
27DAP/17DAP	1.09518	0.879
39DAP/27DAP	0.94018	0.663
41DAP/39DAP	1.26795	0.685
42DAP/41DAP	0.94368	1
43DAP/42DAP	1.01138	0.912
47DAP/43DAP	0.97229	0.876
52DAP/47DAP	1.27105	0.806
57DAP/52DAP	1.06546	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02297	1
17DAP/reference	1.20888	0.036
27DAP/reference	1.04017	0.771
39DAP/reference	1.07281	0.593
41DAP/reference	1.22762	0.032
42DAP/reference	0.92857	0.095
43DAP/reference	1.08227	0.142
47DAP/reference	0.8494	0.035
52DAP/reference	0.92358	0.082
57DAP/reference	0.7902	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05217	0.749
27DAP/17DAP	1.10889	0.653
39DAP/27DAP	0.85639	0.204
41DAP/39DAP	1.09619	0.801
42DAP/41DAP	0.8395	0.106
43DAP/42DAP	0.94004	0.367
47DAP/43DAP	1.10506	0.873
52DAP/47DAP	1.16613	0.471
57DAP/52DAP	1.11795	0.504
57DAP/7DAP	1.0743	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17154	0.235
17DAP/reference	1.53731	0.018
27DAP/reference	1.39111	0.009
39DAP/reference	1.60202	0.022
41DAP/reference	1.27802	0.077
42DAP/reference	1.30518	0.076
43DAP/reference	1.70921	0.006
47DAP/reference	1.08066	0.618
52DAP/reference	1.48655	0.012
57DAP/reference	1.57343	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13358	0.491
17DAP/reference	1.22298	0.07
27DAP/reference	1.02847	1
39DAP/reference	0.84964	0.14
41DAP/reference	1.08363	0.781
42DAP/reference	0.83319	0.032
43DAP/reference	1.12445	0.719
47DAP/reference	0.97425	0.379
52DAP/reference	1.02728	1
57DAP/reference	1.23137	0.523

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.41021	0.025
17DAP/reference	1.21126	0.273
27DAP/reference	1.71308	0.034
39DAP/reference	1.62034	0.005
41DAP/reference	1.26429	0.093
42DAP/reference	1.30825	0.121
43DAP/reference	1.35842	0.029
47DAP/reference	0.83844	0.249
52DAP/reference	1.29811	0.457
57DAP/reference	1.08945	0.873

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01819	1
26DAP/20DAP	0.96135	1
34DAP/26DAP	1.10861	0.542
51DAP/34DAP	1.53442	0.365
52DAP/51DAP	1.24231	0.616
53DAP/52DAP	0.83247	0.649
55DAP/53DAP	1.49777	0.2
57DAP/55DAP	1.03082	0.947
62DAP/57DAP	1.26711	0.393
68DAP/62DAP	1.06374	0.872
68DAP/14DAP	0.51189	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.16802	0.172

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.32574

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90532	0.708
1-1-2/M82	0.85959	0.958
12-2/M82	1.10148	1
12-4/M82	1.10909	0.655
1-3/M82	0.80054	0.441
2-1-1/M82	1.09113
2-1/M82	N/A	N/A
2-6/M82	1.05881	0.425
3-2/M82	N/A	N/A
4-1-1/M82	0.94016	1
4-1/M82	1.1409
4-3-2/M82	0.98732
4-3/M82	0.95782
5-3/M82	0.95856	1
6-2/M82	0.88654	1
6-3/M82	0.98412	1
7-1/M82	N/A	N/A
7-2/M82	0.97594	0.881
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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.90515
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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97403	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.0291	1
DC3000/delta hrp 24h	3.86154	0.018

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	2.54641

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	1.04053	1

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

hybridization	ratio	FDR (corrected p value)
self-self	2.17244	1
Var 0h	0.94871	0.457
Var 12h I row2-row1	0.92394	0.338
Var 12h NI row2-row1	0.96584	0.906
Var 36h I row2-row1	1.08061	0.908
Var 36h NI row2-row1	0.86753	0.645
Var 60h I row2-row1	1.01589	1
Var 60h NI row2-row1	0.96068	1
Time course 0hI-0hNI	1.20485	0.262
Time course 12hI-12hNI	0.94956	0.624
Time course 36hI-36hNI	0.91282	0.132
Time course 60hI-60hNI	1.03976	0.673

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)	1.05176	0.455
transgenic ySAMdc/azygous control (breaker)	1.01525	1
transgenic ySAMdc/azygous control (red)	1.45141	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95945	0.128

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.4361	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71684	1
Manapal/WT (break)	0.85646	0.333
Manapal/WT (red)	0.95041	0.607