Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.11.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92374	0.31
27DAP/17DAP	0.97192	0.966
39DAP/27DAP	1.44842	0.1
41DAP/39DAP	1.06663	0.676
42DAP/41DAP	1.01116	1
43DAP/42DAP	1.02579	1
47DAP/43DAP	0.9268	0.736
52DAP/47DAP	1.30887	0.351
57DAP/52DAP	1.14394	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93724	0.2
17DAP/reference	0.99339	0.777
27DAP/reference	0.95648	0.257
39DAP/reference	0.95713	0.513
41DAP/reference	0.96826	0.542
42DAP/reference	0.96659	0.145
43DAP/reference	0.99601	0.882
47DAP/reference	0.94692	0.09
52DAP/reference	0.97302	0.449
57DAP/reference	0.92708	0.138

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07236	0.365
27DAP/17DAP	0.99905	1
39DAP/27DAP	1.00679	0.832
41DAP/39DAP	0.90176	0.481
42DAP/41DAP	1.0956	0.487
43DAP/42DAP	0.97093	0.751
47DAP/43DAP	1.0325	0.848
52DAP/47DAP	0.98811	0.925
57DAP/52DAP	1.00972	1
57DAP/7DAP	1.14123	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20226	0.138
17DAP/reference	1.08042	0.049
27DAP/reference	1.07373	0.011
39DAP/reference	1.17716	0.014
41DAP/reference	1.12165	0.046
42DAP/reference	1.26865	0.007
43DAP/reference	1.181	0.008
47DAP/reference	1.20807	0.063
52DAP/reference	1.18263	0.013
57DAP/reference	1.07627	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99368	0.848
17DAP/reference	0.95697	0.279
27DAP/reference	1.15858	0.798
39DAP/reference	0.99733	0.702
41DAP/reference	1.09545	0.96
42DAP/reference	0.96424	0.289
43DAP/reference	0.99135	0.774
47DAP/reference	0.98097	0.349
52DAP/reference	0.88003	0.004
57DAP/reference	0.96029	0.208

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99821	0.804
17DAP/reference	0.95958	0.342
27DAP/reference	1.01711	0.903
39DAP/reference	1.06581	0.451
41DAP/reference	1.03886	0.369
42DAP/reference	1.10904	0.114
43DAP/reference	1.01839	0.79
47DAP/reference	0.95242	0.168
52DAP/reference	1.12933	0.301
57DAP/reference	0.8548	0.071

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95743	1
26DAP/20DAP	1.04071	1
34DAP/26DAP	0.88631	0.462
51DAP/34DAP	1.01547	0.962
52DAP/51DAP	1.04105	0.606
53DAP/52DAP	1.03751	0.83
55DAP/53DAP	0.99142	0.894
57DAP/55DAP	1.02342	0.968
62DAP/57DAP	1.2209	0.723
68DAP/62DAP	1.05976	0.899
68DAP/14DAP	0.89504	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.30784	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.40752	0.068
Mature Green Tomato/Ripe Tomato	1.54082
Immature Eggplant/Mature Eggplant	1.29925	0.066
Ripe Pepper/Ripe Tomato	0.47591	0.224
Mature Eggplant/Ripe Tomato	0.42059	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96895	0.944
1-1-2/M82	1.02259	1
12-2/M82	1.03974	1
12-4/M82	1.08437	1
1-3/M82	1.26625	0.277
2-1-1/M82	1.01181	1
2-1/M82	0.92624	0.519
2-6/M82	0.92397	1
3-2/M82	0.99225	1
4-1-1/M82	0.97132	1
4-1/M82	0.74983	0.867
4-3-2/M82	1.11926	1
4-3/M82	0.97886	1
5-3/M82	1.00905	1
6-2/M82	0.9803	1
6-3/M82	1.03859	1
7-1/M82	0.97427
7-2/M82	1.1223	1
9-3-2/M82	1.2374	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05991	1
IL12-4/WTpooled	0.64416
IL1-4/WTpooled	0.98144
WT/WTpooled	0.94609

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	0.95215	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96031	1
DC3000/delta hrp 6h	1.09399	1
DC3000/delta hrp 12h	1.10431	1
DC3000/delta hrp 24h	1.15339	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.13013	0.11
DC3000 delta B/DC3000 delta AB	1.14635	0.23

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.64939	1
Exp 36h	1.39596	0.693
Exp 60h	1.21605	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00797	1
Var 0h	1.23767	0.252
Var 12h I row2-row1	1.01573	0.506
Var 12h NI row2-row1	1.12854	1
Var 36h I row2-row1	1.09976	0.304
Var 36h NI row2-row1	0.97237	0.645
Var 60h I row2-row1	0.87131	0.439
Var 60h NI row2-row1	0.8395	0.69
Time course 0hI-0hNI	1.09061	0.413
Time course 12hI-12hNI	1.00647	0.892
Time course 36hI-36hNI	1.30987	0.006
Time course 60hI-60hNI	1.98635	0.009

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)	1.07341	0.297
transgenic ySAMdc/azygous control (breaker)	0.61886	0.131
transgenic ySAMdc/azygous control (red)	1.00589	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.10445	0.039

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.15078	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88552	1
Manapal/WT (break)	0.86869	1
Manapal/WT (red)	0.40765	0.181