Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.2.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06373	0.961
27DAP/17DAP	1.13354	0.895
39DAP/27DAP	1.22466	0.729
41DAP/39DAP	0.99909	0.92
42DAP/41DAP	1.03758	1
43DAP/42DAP	0.95564	0.9
47DAP/43DAP	0.95145	0.788
52DAP/47DAP	1.68127	0.374
57DAP/52DAP	1.08732	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94754	0.188
17DAP/reference	1.07728	0.294
27DAP/reference	0.90468	0.095
39DAP/reference	1.00207	1
41DAP/reference	1.11257	0.036
42DAP/reference	0.98851	0.469
43DAP/reference	0.97366	0.675
47DAP/reference	0.94357	0.137
52DAP/reference	0.85518	0.075
57DAP/reference	0.95318	0.262

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01071	0.871
27DAP/17DAP	1.21224	0.476
39DAP/27DAP	1.03342	0.758
41DAP/39DAP	1.3361	0.19
42DAP/41DAP	0.81777	0.071
43DAP/42DAP	1.01867	1
47DAP/43DAP	1.29429	0.076
52DAP/47DAP	0.87461	0.482
57DAP/52DAP	1.00924	0.869
57DAP/7DAP	1.62178	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11278	0.589
17DAP/reference	1.01784	1
27DAP/reference	1.15798	0.131
39DAP/reference	1.26481	0.21
41DAP/reference	0.97784	0.538
42DAP/reference	0.97847	0.531
43DAP/reference	0.90287	0.151
47DAP/reference	1.2408	0.026
52DAP/reference	1.10807	0.375
57DAP/reference	1.20221	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02403	0.903
17DAP/reference	1.04808	0.739
27DAP/reference	0.83698	0.155
39DAP/reference	0.97014	0.243
41DAP/reference	0.92883	0.183
42DAP/reference	0.99019	0.594
43DAP/reference	1.14324	0.453
47DAP/reference	0.9755	0.434
52DAP/reference	1.07223	0.322
57DAP/reference	1.13606	0.286

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04563	0.846
17DAP/reference	1.04378	0.767
27DAP/reference	1.12974	0.188
39DAP/reference	1.0781	0.563
41DAP/reference	1.16445	0.239
42DAP/reference	1.02424	1
43DAP/reference	1.21394	0.092
47DAP/reference	0.93669	0.315
52DAP/reference	1.11637	0.517
57DAP/reference	0.90202	0.131

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93386	1
26DAP/20DAP	0.9584	1
34DAP/26DAP	1.82676
51DAP/34DAP	0.83205	0.394
52DAP/51DAP	0.95721	1
53DAP/52DAP	1.04588	0.895
55DAP/53DAP	1.7952	0.027
57DAP/55DAP	1.23477	1
62DAP/57DAP	1.29256	0.04
68DAP/62DAP	0.87719	0.7
68DAP/14DAP	0.83886	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.21861	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.38537	0.814
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06722
1-1-2/M82	0.92463
12-2/M82	N/A	N/A
12-4/M82	1.26938
1-3/M82	0.6918	0.378
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	1.20381
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.88155	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.98901
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	0.98208	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.03226	1
IL12-4/WTpooled	0.9224	0.71
IL1-4/WTpooled	0.78569
WT/WTpooled	1.1439	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	1.57131	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04675	0.921
DC3000/delta hrp 6h	1.71732	1
DC3000/delta hrp 12h	1.16539	1
DC3000/delta hrp 24h	0.95487	0.808

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	1.44657	1
Exp 36h	1.54731	0.349
Exp 60h	1.54004	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97428	1
Var 0h	1.08656	0.98
Var 12h I row2-row1	1.00847	1
Var 12h NI row2-row1	1.14744	0.235
Var 36h I row2-row1	0.94101	1
Var 36h NI row2-row1	0.78131	0.469
Var 60h I row2-row1	0.86917	0.832
Var 60h NI row2-row1	0.73037	0.292
Time course 0hI-0hNI	1.10429	0.852
Time course 12hI-12hNI	1.72824	0.01
Time course 36hI-36hNI	4.83476	0.004
Time course 60hI-60hNI	12.4984	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)	0.92578	0.454
transgenic ySAMdc/azygous control (breaker)	0.58449	0.139
transgenic ySAMdc/azygous control (red)	1.02613	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.11356	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.40037	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98478	0.105
Manapal/WT (break)	1.15374	1
Manapal/WT (red)	1.5363	0.222