Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.1.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.36736	0.014
27DAP/17DAP	0.79879	0.359
39DAP/27DAP	1.3902	0.287
41DAP/39DAP	0.79629	0.225
42DAP/41DAP	1.67487	0.228
43DAP/42DAP	1.44544	0.772
47DAP/43DAP	0.9928	0.868
52DAP/47DAP	0.81595	0.508
57DAP/52DAP	1.09572	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44325	0.01
17DAP/reference	0.9762	0.448
27DAP/reference	1.04062	0.735
39DAP/reference	1.02455	0.857
41DAP/reference	0.96338	0.434
42DAP/reference	1.41105	0.001
43DAP/reference	1.08221	0.403
47DAP/reference	1.45566	0.001
52DAP/reference	1.1713	0.32
57DAP/reference	1.18264	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.44762	0.022
27DAP/17DAP	1.23184	0.113
39DAP/27DAP	1.11262	0.447
41DAP/39DAP	0.53984	0.013
42DAP/41DAP	1.25615	0.308
43DAP/42DAP	2.46664	0.013
47DAP/43DAP	0.98361	0.919
52DAP/47DAP	1.15069	0.616
57DAP/52DAP	1.00786	0.862
57DAP/7DAP	0.87449	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59249	0.024
17DAP/reference	1.16186	0.134
27DAP/reference	0.79896	0.01
39DAP/reference	0.91839	0.146
41DAP/reference	0.79506	0.02
42DAP/reference	0.84989	0.222
43DAP/reference	0.71092	0.019
47DAP/reference	0.95845	0.504
52DAP/reference	0.54826	0.011
57DAP/reference	0.44476	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69054	0.042
17DAP/reference	1.67503	0.007
27DAP/reference	1.20907	0.292
39DAP/reference	1.10192	0.543
41DAP/reference	0.92634	0.291
42DAP/reference	1.19311	0.079
43DAP/reference	0.99407	0.67
47DAP/reference	1.02711	1
52DAP/reference	1.07046	0.194
57DAP/reference	0.8497	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04372	0.532
17DAP/reference	1.18248	0.273
27DAP/reference	0.87649	0.046
39DAP/reference	0.86225	0.076
41DAP/reference	0.78997	0.086
42DAP/reference	1.53652	0.127
43DAP/reference	1.24175	0.412
47DAP/reference	0.95168	0.357
52DAP/reference	0.66277	0.066
57DAP/reference	1.08217	0.873

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.3097	0.966
26DAP/20DAP	0.98261	1
34DAP/26DAP	1.11047	1
51DAP/34DAP	0.86188	0.508
52DAP/51DAP	1.7709	0.039
53DAP/52DAP	0.84843	0.379
55DAP/53DAP	1.289	0.075
57DAP/55DAP	0.73372	0.09
62DAP/57DAP	1.03543	0.935
68DAP/62DAP	1.30507	0.491
68DAP/14DAP	1.18566	0.802

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.16069	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.07323
Mature Green Tomato/Ripe Tomato	0.81902	0.021
Immature Eggplant/Mature Eggplant	2.11078	0.05
Ripe Pepper/Ripe Tomato	0.07484	0.224
Mature Eggplant/Ripe Tomato	0.24232	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.37052	0.551
1-1-2/M82	1.53768	1
12-2/M82	3.23073	1
12-4/M82	1.47451	1
1-3/M82	1.97323	0.248
2-1-1/M82	1.04081	0.689
2-1/M82	0.87357	0.74
2-6/M82	1.11254	0.425
3-2/M82	1.16487	0.84
4-1-1/M82	1.36911	1
4-1/M82	N/A	N/A
4-3-2/M82	1.53515	0.241
4-3/M82	1.55771	1
5-3/M82	0.9288	1
6-2/M82	1.24185	1
6-3/M82	1.11898	1
7-1/M82	1.00975	1
7-2/M82	1.1978	0.385
9-3-2/M82	1.75987	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	0.86218
IL12-4/WTpooled	0.63721	0.566
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	0.91371

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	0.97948	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00887	1
DC3000/delta hrp 6h	0.95628	0.95
DC3000/delta hrp 12h	1.48658	1
DC3000/delta hrp 24h	0.63796	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17269	0.384
DC3000 delta B/DC3000 delta AB	1.5385	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98734	1
Exp 36h	1.00742	1
Exp 60h	1.00298	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99706	1
Var 0h	1.14511	0.98
Var 12h I row2-row1	1.03624	1
Var 12h NI row2-row1	1.14016	0.649
Var 36h I row2-row1	1.27934	1
Var 36h NI row2-row1	0.98626	0.852
Var 60h I row2-row1	1.09512	1
Var 60h NI row2-row1	0.99032	1
Time course 0hI-0hNI	0.84858	0.178
Time course 12hI-12hNI	0.80141	0.033
Time course 36hI-36hNI	1.10312	0.632
Time course 60hI-60hNI	0.59113	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)	1.04744	0.654
transgenic ySAMdc/azygous control (breaker)	1.09792	1
transgenic ySAMdc/azygous control (red)	0.96325	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93246	0.043

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21263	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.11222	0.088
Manapal/WT (break)	1.1245	0.14
Manapal/WT (red)	0.98814	0.863