Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.10.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05395	1
27DAP/17DAP	1.32037	0.793
39DAP/27DAP	1.1843	0.745
41DAP/39DAP	1.68938	0.488
42DAP/41DAP	1.31327	0.681
43DAP/42DAP	1.28202	0.772
47DAP/43DAP	1.15407	0.873
52DAP/47DAP	0.98644	0.854
57DAP/52DAP	0.99281	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77304	0.028
17DAP/reference	1.06891	0.675
27DAP/reference	0.91831	0.339
39DAP/reference	0.97214	0.6
41DAP/reference	0.745	0.009
42DAP/reference	0.78362	0.009
43DAP/reference	0.97841	0.708
47DAP/reference	0.75387	0.05
52DAP/reference	0.79974	0.02
57DAP/reference	0.88796	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11922	0.431
27DAP/17DAP	1.18796	0.362
39DAP/27DAP	0.73573	0.181
41DAP/39DAP	0.99834	1
42DAP/41DAP	0.91271	0.466
43DAP/42DAP	0.89402	0.399
47DAP/43DAP	0.9876	0.939
52DAP/47DAP	1.27428	0.441
57DAP/52DAP	1.22455	0.457
57DAP/7DAP	1.39601	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1121	0.638
17DAP/reference	0.93349	0.167
27DAP/reference	0.85807	0.055
39DAP/reference	0.98216	0.474
41DAP/reference	1.15381	0.375
42DAP/reference	0.94668	0.355
43DAP/reference	0.82449	0.047
47DAP/reference	0.88021	0.293
52DAP/reference	0.94466	0.363
57DAP/reference	0.90716	0.232

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83762	0.129
17DAP/reference	0.97281	0.474
27DAP/reference	0.97863	0.554
39DAP/reference	0.80454	0.042
41DAP/reference	0.92131	0.284
42DAP/reference	0.90316	0.321
43DAP/reference	1.15415	0.865
47DAP/reference	0.90577	0.188
52DAP/reference	0.9033	0.259
57DAP/reference	1.00207	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97977	0.455
17DAP/reference	1.02457	0.966
27DAP/reference	0.86672	0.049
39DAP/reference	0.84243	0.019
41DAP/reference	0.91098	0.05
42DAP/reference	0.98684	0.816
43DAP/reference	0.75017	0.049
47DAP/reference	0.94333	0.396
52DAP/reference	0.83837	0.208
57DAP/reference	0.71469	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.59969	0.52
26DAP/20DAP	0.91571	1
34DAP/26DAP	1.12777	1
51DAP/34DAP	1.07931	1
52DAP/51DAP	1.04173	1
53DAP/52DAP	1.40546	0.319
55DAP/53DAP	1.33133	0.067
57DAP/55DAP	1.3928	0.793
62DAP/57DAP	0.71617	0.003
68DAP/62DAP	0.86436	0.668
68DAP/14DAP	0.8242	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.31687	0.865

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	1.85363	0.311
Ripe Pepper/Ripe Tomato	0.58716	0.293
Mature Eggplant/Ripe Tomato	0.65428	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	0.86055	1
1-3/M82	N/A	N/A
2-1-1/M82	0.97922
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.18977
4-3/M82	1.65333	0.268
5-3/M82	1.13898	1
6-2/M82	N/A	N/A
6-3/M82	1.029
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	0.74685

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03309	1
IL2-6/WTpooled	1.13903	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01332	1
IL12-4/WTpooled	0.65435	0.581
IL1-4/WTpooled	1.17093	1
WT/WTpooled	0.94213	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	0.79526	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.06954	0.921
DC3000/delta hrp 6h	0.93903	0.95
DC3000/delta hrp 12h	1.09668	1
DC3000/delta hrp 24h	0.66243	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.4727	0.025
DC3000 delta B/DC3000 delta AB	0.52269	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.92564	1
Exp 36h	0.62155	0.406
Exp 60h	0.602	0.266

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00462	1
Var 0h	0.53529	0.936
Var 12h I row2-row1	0.8224	0.338
Var 12h NI row2-row1	1.02716	0.649
Var 36h I row2-row1	1.02263	1
Var 36h NI row2-row1	1.48813	1
Var 60h I row2-row1	1.56042	1
Var 60h NI row2-row1	0.99678	1
Time course 0hI-0hNI	0.99154	1
Time course 12hI-12hNI	0.9279	0.177
Time course 36hI-36hNI	0.81905	0.025
Time course 60hI-60hNI	0.26179	0.006

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)	1.31688	0.273
transgenic ySAMdc/azygous control (breaker)	1.15263	0.248
transgenic ySAMdc/azygous control (red)	1.15034	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96606	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.62385	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.86887	0.096
Manapal/WT (break)	1.27059	0.381
Manapal/WT (red)	1.06861	1