Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.17.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78186	0.297
27DAP/17DAP	1.07022	1
39DAP/27DAP	2.143	0.045
41DAP/39DAP	1.07652	0.822
42DAP/41DAP	1.38046	0.366
43DAP/42DAP	0.98003	0.89
47DAP/43DAP	1.17287	0.727
52DAP/47DAP	0.65151	0.172
57DAP/52DAP	1.14774	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24734	0.994
17DAP/reference	0.98927	0.858
27DAP/reference	1.12232	0.66
39DAP/reference	0.84591	0.064
41DAP/reference	0.85988	0.267
42DAP/reference	1.03498	1
43DAP/reference	1.12563	0.471
47DAP/reference	1.18883	0.148
52DAP/reference	1.42764	0.092
57DAP/reference	1.28412	0.073

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.77994	0.323
27DAP/17DAP	1.11953	0.887
39DAP/27DAP	1.42582	0.27
41DAP/39DAP	1.55715	0.407
42DAP/41DAP	0.99668	0.777
43DAP/42DAP	1.06734	0.413
47DAP/43DAP	1.16288	0.552
52DAP/47DAP	0.88016	0.466
57DAP/52DAP	1.00685	0.862
57DAP/7DAP	1.00865	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2782	0.039
17DAP/reference	0.74415	0.013
27DAP/reference	0.86553	0.013
39DAP/reference	0.69437	0.013
41DAP/reference	0.71361	0.033
42DAP/reference	0.8134	0.032
43DAP/reference	0.74112	0.04
47DAP/reference	0.72298	0.101
52DAP/reference	0.73679	0.015
57DAP/reference	0.61283	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17079	0.885
17DAP/reference	0.69318	0.008
27DAP/reference	0.91774	0.407
39DAP/reference	1.10813	1
41DAP/reference	1.16999	0.513
42DAP/reference	1.05654	0.723
43DAP/reference	0.77725	0.033
47DAP/reference	1.04531	0.795
52DAP/reference	1.15141	0.789
57DAP/reference	0.91923	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38962	0.016
17DAP/reference	0.78818	0.221
27DAP/reference	0.66047	0.044
39DAP/reference	0.92114	0.147
41DAP/reference	0.81963	0.046
42DAP/reference	0.98262	0.671
43DAP/reference	1.01148	1
47DAP/reference	0.91905	0.259
52DAP/reference	0.87465	0.327
57DAP/reference	0.92968	0.43

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.87111	1
26DAP/20DAP	1.50425
34DAP/26DAP	0.7316	0.404
51DAP/34DAP	1.72806
52DAP/51DAP	1.1304	0.733
53DAP/52DAP	2.01853	0.221
55DAP/53DAP	1.04074	0.864
57DAP/55DAP	0.96972	0.825
62DAP/57DAP	0.96539	0.994
68DAP/62DAP	1.33464	0.464
68DAP/14DAP	0.80761

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.3293	0.047

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.60002	0.256
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.12455	1
Mature Eggplant/Ripe Tomato	0.25172	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02801	0.742
1-1-2/M82	1.15054	1
12-2/M82	0.67813
12-4/M82	1.16486	1
1-3/M82	1.88629
2-1-1/M82	1.13589
2-1/M82	0.92306
2-6/M82	1.94169	0.345
3-2/M82	1.03527
4-1-1/M82	1.84742	0.963
4-1/M82	1.27068	1
4-3-2/M82	1.15443
4-3/M82	1.03155	1
5-3/M82	0.92163	0.419
6-2/M82	1.33947
6-3/M82	0.36429
7-1/M82	1.01823
7-2/M82	1.6362	0.282
9-3-2/M82	2.50647

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.94942	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.945	1
IL12-4/WTpooled	1.27054	0.516
IL1-4/WTpooled	0.85808	0.435
WT/WTpooled	1.0698	0.89

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	1.57752	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05812	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.10231
DC3000/delta hrp 24h	3.18791	0.022

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	1.27164	1
Exp 36h	N/A	N/A
Exp 60h	1.53025	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.81974	1
Var 0h	1.26349	0.289
Var 12h I row2-row1	1.13574	0.473
Var 12h NI row2-row1	2.30634	1
Var 36h I row2-row1	1.20828	0.309
Var 36h NI row2-row1	1.17757	0.482
Var 60h I row2-row1	1.05382	1
Var 60h NI row2-row1	0.72383	1
Time course 0hI-0hNI	1.18574	0.63
Time course 12hI-12hNI	1.43868	0.015
Time course 36hI-36hNI	1.66238	0.005
Time course 60hI-60hNI	3.51591	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	1.3829	1
transgenic ySAMdc/azygous control (red)	1.12813	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.48295	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.95122	1
Manapal/WT (red)	1.18412	0.413