Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1766	0.827
27DAP/17DAP	1.3013	0.801
39DAP/27DAP	0.91505	0.564
41DAP/39DAP	1.36013	0.498
42DAP/41DAP	1.00187	1
43DAP/42DAP	1.14967	0.968
47DAP/43DAP	0.93226	0.693
52DAP/47DAP	1.45534	0.52
57DAP/52DAP	1.25378	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93352	0.194
17DAP/reference	0.94384	0.069
27DAP/reference	0.97324	0.567
39DAP/reference	0.98233	0.734
41DAP/reference	1.04528	0.48
42DAP/reference	0.95121	0.111
43DAP/reference	0.99527	0.861
47DAP/reference	0.90989	0.014
52DAP/reference	0.89997	0.075
57DAP/reference	0.92768	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94788	0.388
27DAP/17DAP	0.97134	0.878
39DAP/27DAP	1.01401	0.811
41DAP/39DAP	1.09187	0.603
42DAP/41DAP	0.99036	0.858
43DAP/42DAP	1.02948	0.627
47DAP/43DAP	1.04222	0.485
52DAP/47DAP	1.05711	0.8
57DAP/52DAP	1.02522	0.906
57DAP/7DAP	1.14618	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93832	0.088
17DAP/reference	0.90382	0.017
27DAP/reference	0.90861	0.018
39DAP/reference	0.91379	0.02
41DAP/reference	0.82067	0.032
42DAP/reference	0.7926	0.01
43DAP/reference	0.8546	0.042
47DAP/reference	0.88736	0.383
52DAP/reference	0.8053	0.057
57DAP/reference	0.80031	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04478	0.55
17DAP/reference	0.96974	0.434
27DAP/reference	0.88337	0.16
39DAP/reference	0.94616	0.314
41DAP/reference	0.81262	0.021
42DAP/reference	0.92189	0.189
43DAP/reference	1.04434	0.662
47DAP/reference	1.00082	0.833
52DAP/reference	0.86903	0.047
57DAP/reference	0.97429	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.909	0.038
17DAP/reference	0.97364	0.374
27DAP/reference	0.91333	0.119
39DAP/reference	0.94125	0.02
41DAP/reference	0.95081	0.371
42DAP/reference	0.92851	0.22
43DAP/reference	0.91224	0.197
47DAP/reference	0.97591	0.465
52DAP/reference	0.9571	0.444
57DAP/reference	0.75001	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17362	0.966
26DAP/20DAP	1.14986	0.464
34DAP/26DAP	0.99273	1
51DAP/34DAP	1.01394	0.962
52DAP/51DAP	1.0382	0.556
53DAP/52DAP	0.98133	0.897
55DAP/53DAP	1.00827	0.951
57DAP/55DAP	1.32752	0.097
62DAP/57DAP	0.99031	0.994
68DAP/62DAP	0.95638	0.769
68DAP/14DAP	0.91057	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15714	0.264

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.64574	0.162
Mature Green Tomato/Ripe Tomato	1.02061	0.948
Immature Eggplant/Mature Eggplant	0.92045	0.545
Ripe Pepper/Ripe Tomato	1.92288	0.258
Mature Eggplant/Ripe Tomato	0.72484	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97423	0.961
1-1-2/M82	1.01493	1
12-2/M82	1.06906	1
12-4/M82	1.01336	1
1-3/M82	1.66601	1
2-1-1/M82	1.17791	0.764
2-1/M82	0.8278	0.519
2-6/M82	0.99952	1
3-2/M82	1.00427	1
4-1-1/M82	1.05294	1
4-1/M82	1.11035	0.853
4-3-2/M82	1.18988	0.508
4-3/M82	1.07759	1
5-3/M82	1.04497	1
6-2/M82	1.25154	1
6-3/M82	0.97833	1
7-1/M82	1.06184	0.925
7-2/M82	1.03136	1
9-3-2/M82	1.16997	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.02898	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13252	1
IL12-4/WTpooled	0.95868	1
IL1-4/WTpooled	1.18057	0.426
WT/WTpooled	0.96304	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	0.89254	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01878	0.921
DC3000/delta hrp 6h	0.86538	0.95
DC3000/delta hrp 12h	1.20769	1
DC3000/delta hrp 24h	1.12717	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.18862	0.053
DC3000 delta B/DC3000 delta AB	1.13174	0.269

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9472	0.24
Exp 36h	1.61264	1
Exp 60h	1.67522	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96396	1
Var 0h	1.04719	1
Var 12h I row2-row1	1.04355	0.692
Var 12h NI row2-row1	1.04549	1
Var 36h I row2-row1	1.04347	1
Var 36h NI row2-row1	0.85842	0.522
Var 60h I row2-row1	0.99192	1
Var 60h NI row2-row1	1.05068	1
Time course 0hI-0hNI	1.12145	0.662
Time course 12hI-12hNI	0.99891	1
Time course 36hI-36hNI	1.07146	0.401
Time course 60hI-60hNI	1.78577	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)	0.87502	0.246
transgenic ySAMdc/azygous control (breaker)	0.9316	0.49
transgenic ySAMdc/azygous control (red)	1.06223	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03813	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82547	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96051	1
Manapal/WT (break)	0.73555	0.299
Manapal/WT (red)	0.97981	0.863