Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.3.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86171	0.413
27DAP/17DAP	1.56761	0.587
39DAP/27DAP	0.92619	0.663
41DAP/39DAP	0.87038	0.539
42DAP/41DAP	0.99314	1
43DAP/42DAP	0.99233	0.937
47DAP/43DAP	1.1581	0.95
52DAP/47DAP	0.77457	0.508
57DAP/52DAP	1.24783	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98473	0.601
17DAP/reference	0.90967	0.208
27DAP/reference	0.9568	0.359
39DAP/reference	0.82135	0.014
41DAP/reference	0.77371	0.014
42DAP/reference	0.96094	0.233
43DAP/reference	0.96015	0.691
47DAP/reference	1.02011	0.963
52DAP/reference	1.21961	0.092
57DAP/reference	1.17871	0.033

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10625	0.847
27DAP/17DAP	1.06714	0.881
39DAP/27DAP	0.82471	0.311
41DAP/39DAP	1.18652	0.238
42DAP/41DAP	0.79583	0.051
43DAP/42DAP	1.07246	0.627
47DAP/43DAP	0.96984	0.861
52DAP/47DAP	1.08613	0.766
57DAP/52DAP	0.80407	0.138
57DAP/7DAP	1.12245	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.56344	0.051
17DAP/reference	1.65206	0.008
27DAP/reference	1.27832	0.009
39DAP/reference	1.27122	0.024
41DAP/reference	1.23437	0.104
42DAP/reference	1.51065	0.01
43DAP/reference	1.43558	0.007
47DAP/reference	1.0947	0.468
52DAP/reference	1.42534	0.021
57DAP/reference	1.54677	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89555	0.14
17DAP/reference	0.94268	0.367
27DAP/reference	1.00443	0.765
39DAP/reference	1.03988	0.935
41DAP/reference	1.11886	0.344
42DAP/reference	0.95957	0.289
43DAP/reference	0.86403	0.186
47DAP/reference	0.93341	0.178
52DAP/reference	1.02633	0.988
57DAP/reference	0.84853	0.092

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42272	0.072
17DAP/reference	1.21828	0.712
27DAP/reference	1.6195	0.041
39DAP/reference	1.24232	0.12
41DAP/reference	1.42331	0.056
42DAP/reference	1.30322	0.08
43DAP/reference	1.26421	0.045
47DAP/reference	0.90475	0.306
52DAP/reference	1.2727	0.575
57DAP/reference	1.44215	0.029

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.26759	0.966
26DAP/20DAP	1.07626
34DAP/26DAP	1.8694	0.819
51DAP/34DAP	0.85033	0.492
52DAP/51DAP	1.05047
53DAP/52DAP	1.18491	0.428
55DAP/53DAP	1.11309	0.826
57DAP/55DAP	1.11658	1
62DAP/57DAP	1.14688	0.217
68DAP/62DAP	0.47879
68DAP/14DAP	2.25952	0.031

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.75986	0.113

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.50194	0.267
Immature Eggplant/Mature Eggplant	0.04191	1
Ripe Pepper/Ripe Tomato	0.51436	0.293
Mature Eggplant/Ripe Tomato	0.35497	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.0298
12-2/M82	2.15284
12-4/M82	1.08331
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
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	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.66792
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.61797

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.87681	0.321
IL2-6/WTpooled	0.90267	1
IL7-5/WTpooled	0.87281	0.559
IL7-3/WTpooled	0.8525	0.418
IL12-4/WTpooled	0.84754	0.71
IL1-4/WTpooled	0.99568	1
WT/WTpooled	0.9658	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	1.69599	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85126
DC3000/delta hrp 6h	1.51033	1
DC3000/delta hrp 12h	0.76739	1
DC3000/delta hrp 24h	2.53429	0.024

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	3.07877	0.042
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	1.35398	1
Exp 36h	N/A	N/A
Exp 60h	1.952	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03299	1
Var 0h	0.97503	1
Var 12h I row2-row1	1.25089
Var 12h NI row2-row1	1.05043
Var 36h I row2-row1	0.9054	1
Var 36h NI row2-row1	0.85864
Var 60h I row2-row1	0.58004
Var 60h NI row2-row1	0.89644	0.292
Time course 0hI-0hNI	1.03461	0.852
Time course 12hI-12hNI	1.13131	0.452
Time course 36hI-36hNI	1.61014	0.005
Time course 60hI-60hNI	2.08051	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)	0.70233	0.289
transgenic ySAMdc/azygous control (breaker)	0.64734	0.173
transgenic ySAMdc/azygous control (red)	1.36543	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04751	0.213

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.60828	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99502	1
Manapal/WT (break)	0.8603	1
Manapal/WT (red)	0.51019	0.181