Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.18.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86811	0.586
27DAP/17DAP	1.29718	0.829
39DAP/27DAP	1.17994	0.82
41DAP/39DAP	0.91737	0.772
42DAP/41DAP	0.7274	0.774
43DAP/42DAP	1.24474	1
47DAP/43DAP	2.01836	0.193
52DAP/47DAP	2.96186	0.032
57DAP/52DAP	1.16718	0.93

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78943	0.033
17DAP/reference	0.8786	0.097
27DAP/reference	0.91191	0.24
39DAP/reference	0.92141	0.184
41DAP/reference	0.95181	0.542
42DAP/reference	0.98379	0.287
43DAP/reference	0.88663	0.084
47DAP/reference	1.13887	0.353
52DAP/reference	1.28624	0.056
57DAP/reference	1.22429	0.07

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.94413	0.132
27DAP/17DAP	1.35097	0.527
39DAP/27DAP	0.8163	0.291
41DAP/39DAP	1.20117	0.727
42DAP/41DAP	0.57315	0.007
43DAP/42DAP	1.1259	0.699
47DAP/43DAP	1.07303	0.833
52DAP/47DAP	1.39382	0.207
57DAP/52DAP	0.90551	0.577
57DAP/7DAP	1.14003	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04141	0.999
17DAP/reference	0.93475	0.295
27DAP/reference	1.09607	0.301
39DAP/reference	1.00816	0.745
41DAP/reference	0.94164	0.326
42DAP/reference	1.21957	0.405
43DAP/reference	1.09655	0.307
47DAP/reference	1.00943	1
52DAP/reference	1.10281	0.401
57DAP/reference	1.24883	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7484	0.012
17DAP/reference	0.65947	0.004
27DAP/reference	0.78172	0.038
39DAP/reference	0.88937	0.129
41DAP/reference	0.89438	0.156
42DAP/reference	0.94993	0.355
43DAP/reference	0.7607	0.036
47DAP/reference	0.85427	0.06
52DAP/reference	0.84744	0.012
57DAP/reference	0.7363	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11573	0.758
17DAP/reference	0.98962	0.763
27DAP/reference	1.23231	0.531
39DAP/reference	1.11396	0.13
41DAP/reference	1.32447	0.12
42DAP/reference	1.0003	1
43DAP/reference	1.06241	0.855
47DAP/reference	0.92039	0.018
52DAP/reference	0.8769	0.296
57DAP/reference	1.19833	0.141

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09648	0.966
26DAP/20DAP	2.11018	0.102
34DAP/26DAP	1.26273	1
51DAP/34DAP	1.27823	0.883
52DAP/51DAP	0.86487	1
53DAP/52DAP	1.00243	0.868
55DAP/53DAP	1.34277	0.781
57DAP/55DAP	0.98403	0.902
62DAP/57DAP	0.93556	0.994
68DAP/62DAP	1.46653	0.481
68DAP/14DAP	1.79303	0.038

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.91258

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.02666	0.014
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.14068	0.224
Mature Eggplant/Ripe Tomato	0.15589	0.234

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	0.99209
1-3/M82	N/A	N/A
2-1-1/M82	0.60587
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.72965
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	0.89726
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.4404
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	1.1028
IL1-4/WTpooled	1.09698	1
WT/WTpooled	1.45032

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	1.21424

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0665	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.128	1
DC3000/delta hrp 24h	0.92366	0.387

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	1.11138	1
Exp 36h	N/A	N/A
Exp 60h	1.10006	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.15659
Var 0h	0.87587	1
Var 12h I row2-row1	1.1108	0.324
Var 12h NI row2-row1	0.85069	1
Var 36h I row2-row1	1.08521	0.298
Var 36h NI row2-row1	1.15093
Var 60h I row2-row1	0.59526	0.285
Var 60h NI row2-row1	0.62067	0.932
Time course 0hI-0hNI	1.08076	0.719
Time course 12hI-12hNI	1.49382	0.327
Time course 36hI-36hNI	1.70409	0.063
Time course 60hI-60hNI	10.1459	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)	0.81094	1
transgenic ySAMdc/azygous control (red)	1.19314	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.97634	0.353

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60912	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.78968	1
Manapal/WT (break)	0.71001	0.299
Manapal/WT (red)	N/A	N/A