Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.12941	0.932
27DAP/17DAP	1.21652	0.813
39DAP/27DAP	1.06302	1
41DAP/39DAP	1.072	0.871
42DAP/41DAP	0.93672	1
43DAP/42DAP	0.9419	0.686
47DAP/43DAP	0.94196	0.788
52DAP/47DAP	1.20619	0.549
57DAP/52DAP	1.0617	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10749	0.334
17DAP/reference	0.98892	0.819
27DAP/reference	1.0278	0.684
39DAP/reference	1.00582	0.92
41DAP/reference	1.08604	0.133
42DAP/reference	1.1984	0.005
43DAP/reference	0.97787	0.708
47DAP/reference	1.1747	0.004
52DAP/reference	1.14474	0.407
57DAP/reference	1.00957	0.671

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90036	0.484
27DAP/17DAP	0.99348	0.943
39DAP/27DAP	0.97429	0.953
41DAP/39DAP	1.19162	0.176
42DAP/41DAP	1.02647	0.929
43DAP/42DAP	0.91724	0.097
47DAP/43DAP	0.99941	1
52DAP/47DAP	0.91109	0.666
57DAP/52DAP	0.87163	0.245
57DAP/7DAP	0.79

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97732	0.203
17DAP/reference	0.99587	0.599
27DAP/reference	0.99366	0.614
39DAP/reference	0.97662	0.027
41DAP/reference	1.04843	0.46
42DAP/reference	1.0796	0.024
43DAP/reference	0.98302	0.48
47DAP/reference	1.19993	0.235
52DAP/reference	1.03959	0.832
57DAP/reference	1.09218	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05266	0.62
17DAP/reference	1.23001	0.035
27DAP/reference	1.26987	0.153
39DAP/reference	1.50153	0.014
41DAP/reference	1.61309	0.014
42DAP/reference	1.41915	0.009
43DAP/reference	1.26068	0.268
47DAP/reference	1.32277	0.01
52DAP/reference	1.34374	0.006
57DAP/reference	1.2199	0.193

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01336	1
17DAP/reference	1.08271	0.394
27DAP/reference	1.05274	0.149
39DAP/reference	1.12591	0.072
41DAP/reference	1.06027	0.537
42DAP/reference	1.06634	0.635
43DAP/reference	1.19851	0.465
47DAP/reference	1.13792	0.093
52DAP/reference	0.95774	0.464
57DAP/reference	1.21597	0.069

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.88195	0.981
26DAP/20DAP	0.90288	0.512
34DAP/26DAP	1.03634	1
51DAP/34DAP	0.95193	0.571
52DAP/51DAP	0.95863	1
53DAP/52DAP	1.14182
55DAP/53DAP	0.98269	0.894
57DAP/55DAP	1.05127	0.935
62DAP/57DAP	1.00424	1
68DAP/62DAP	0.90303	0.722
68DAP/14DAP	0.79012	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.19832	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.65415	0.113
Mature Green Tomato/Ripe Tomato	1.47787	0.166
Immature Eggplant/Mature Eggplant	1.09859	0.363
Ripe Pepper/Ripe Tomato	0.22504	0.224
Mature Eggplant/Ripe Tomato	0.66343

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	0.73805
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	1.03853
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.18883
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
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	0.95913	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.46815	0.277
IL2-6/WTpooled	1.10618	0.419
IL7-5/WTpooled	1.03592	1
IL7-3/WTpooled	1.12285	1
IL12-4/WTpooled	1.16985	0.516
IL1-4/WTpooled	1.14734	1
WT/WTpooled	1.01584	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	1.58948	0.222

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97262	1
DC3000/delta hrp 6h	1.07439	1
DC3000/delta hrp 12h	1.54169	1
DC3000/delta hrp 24h	1.86518	0.056

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.35635	0.042
DC3000 delta B/DC3000 delta AB	1.73018	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22776	1
Exp 36h	0.87516	0.661
Exp 60h	1.13417	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.9809	1
Var 0h	1.37467	0.782
Var 12h I row2-row1	0.71834	0.514
Var 12h NI row2-row1	1.75248	0.34
Var 36h I row2-row1	1.33312	0.601
Var 36h NI row2-row1	0.57688	0.478
Var 60h I row2-row1	0.85092	0.582
Var 60h NI row2-row1	0.72476	0.304
Time course 0hI-0hNI	1.22856	0.574
Time course 12hI-12hNI	1.17434	0.693
Time course 36hI-36hNI	3.57811	0.005
Time course 60hI-60hNI	12.0519	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)	0.79994	0.301
transgenic ySAMdc/azygous control (breaker)	0.69132	0.131
transgenic ySAMdc/azygous control (red)	0.98416	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86145	0.05

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.64744	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32719	0.084
Manapal/WT (break)	0.85189	0.333
Manapal/WT (red)	0.88397	0.607