Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87485	0.405
27DAP/17DAP	0.70255	0.122
39DAP/27DAP	0.7456	0.421
41DAP/39DAP	0.74199	0.15
42DAP/41DAP	0.70025	0.397
43DAP/42DAP	1.18685	0.736
47DAP/43DAP	0.64719	0.109
52DAP/47DAP	1.18193	0.844
57DAP/52DAP	0.72706	0.55

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88336	0.034
17DAP/reference	0.74103	0.029
27DAP/reference	0.84973	0.129
39DAP/reference	0.80383	0.033
41DAP/reference	0.88391	0.542
42DAP/reference	0.86136	0.12
43DAP/reference	0.39723
47DAP/reference	1.03561	0.503
52DAP/reference	0.57889	0.015
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96073	0.629
27DAP/17DAP	0.90762	0.537
39DAP/27DAP	0.66543	0.034
41DAP/39DAP	0.92672	0.512
42DAP/41DAP	0.90803	0.387
43DAP/42DAP	0.59151	0.022
47DAP/43DAP	0.88672	0.207
52DAP/47DAP	1.28719	0.467
57DAP/52DAP	0.99187	0.833
57DAP/7DAP	0.23757	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49073	0.028
17DAP/reference	1.06855	0.328
27DAP/reference	1.04395	0.804
39DAP/reference	0.97291	0.474
41DAP/reference	0.79454	0.02
42DAP/reference	0.92728	0.144
43DAP/reference	0.88597	0.086
47DAP/reference	0.92387	0.504
52DAP/reference	0.74562	0.019
57DAP/reference	0.8083	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07035	0.903
17DAP/reference	0.81176	0.063
27DAP/reference	0.95318	0.438
39DAP/reference	0.93437	0.359
41DAP/reference	0.82674	0.005
42DAP/reference	0.95106	0.289
43DAP/reference	1.08427	0.774
47DAP/reference	0.87273	0.037
52DAP/reference	0.77792	0.009
57DAP/reference	0.5703	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.80012	0.021
17DAP/reference	1.19608	0.243
27DAP/reference	1.00067	0.805
39DAP/reference	1.11126	0.175
41DAP/reference	1.19771	0.181
42DAP/reference	1.16039	0.167
43DAP/reference	0.87985	0.197
47DAP/reference	0.69785	0.005
52DAP/reference	0.79376	0.089
57DAP/reference	1.29435	0.053

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10207	0.966
26DAP/20DAP	0.8164	1
34DAP/26DAP	1.09707	1
51DAP/34DAP	1.29672	0.092
52DAP/51DAP	N/A	N/A
53DAP/52DAP	0.85638	0.316
55DAP/53DAP	0.43786	0.016
57DAP/55DAP	0.89443	0.545
62DAP/57DAP	1.17732	0.868
68DAP/62DAP	1.397	0.142
68DAP/14DAP	1.23191	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.15719	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.33743	0.058
Mature Green Tomato/Ripe Tomato	3.62898	0.015
Immature Eggplant/Mature Eggplant	0.53834	0.067
Ripe Pepper/Ripe Tomato	2.04726	1
Mature Eggplant/Ripe Tomato	3.54882	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.69461
1-1-2/M82	1.40063	1
12-2/M82	0.76711	0.678
12-4/M82	0.82634	0.257
1-3/M82	N/A	N/A
2-1-1/M82	0.84916
2-1/M82	N/A	N/A
2-6/M82	1.59547	0.395
3-2/M82	N/A	N/A
4-1-1/M82	0.87178
4-1/M82	N/A	N/A
4-3-2/M82	1.81661	0.241
4-3/M82	0.66945
5-3/M82	0.90577	0.642
6-2/M82	1.48885	1
6-3/M82	N/A	N/A
7-1/M82	1.29246
7-2/M82	0.90192
9-3-2/M82	1.47343	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.73549	0.247
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.70597	0.635
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.89446
WT/WTpooled	0.82054

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	0.91627	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01591	1
DC3000/delta hrp 6h	0.77176	0.757
DC3000/delta hrp 12h	1.33563	1
DC3000/delta hrp 24h	0.8477	0.269

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.64451	0.024
DC3000 delta B/DC3000 delta AB	0.63711	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.19589	1
Exp 36h	0.81013	0.699
Exp 60h	0.74038	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99575	1
Var 0h	1.04951	0.782
Var 12h I row2-row1	0.72257
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	0.99726	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.01162	0.867
Time course 12hI-12hNI	1.01028	1
Time course 36hI-36hNI	1.01654	0.874
Time course 60hI-60hNI	0.26	0.005

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)	1.26337	0.321
transgenic ySAMdc/azygous control (breaker)	1.1405	1
transgenic ySAMdc/azygous control (red)	1.21298	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98331	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.62907	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.27056	0.096
Manapal/WT (break)	2.41828	0.123
Manapal/WT (red)	2.43212	0.126