Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.14.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.93213	0.037
27DAP/17DAP	0.90627	0.697
39DAP/27DAP	9.19137	0.065
41DAP/39DAP	1.4262	0.603
42DAP/41DAP	2.34853	0.043
43DAP/42DAP	1.6163	0.937
47DAP/43DAP	0.18278	0.04
52DAP/47DAP	0.77704	0.486
57DAP/52DAP	1.02632	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67847	0.044
17DAP/reference	0.78234	0.017
27DAP/reference	0.80184	0.078
39DAP/reference	1.05308	0.889
41DAP/reference	0.93694	0.341
42DAP/reference	1.36946	0.007
43DAP/reference	0.92577	0.088
47DAP/reference	0.86315	0.001
52DAP/reference	0.76419	0.03
57DAP/reference	1.05252	0.259

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.09479	0.036
27DAP/17DAP	0.59703	0.124
39DAP/27DAP	3.488	0.043
41DAP/39DAP	0.62295	0.013
42DAP/41DAP	1.49173	0.006
43DAP/42DAP	1.19281	0.045
47DAP/43DAP	0.55984	0.008
52DAP/47DAP	0.80876	0.247
57DAP/52DAP	0.80083	0.339
57DAP/7DAP	1.15662

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85911	0.091
17DAP/reference	0.96949	0.039
27DAP/reference	0.93718	0.045
39DAP/reference	0.99584	0.745
41DAP/reference	0.93683	0.133
42DAP/reference	0.98304	0.458
43DAP/reference	0.94809	0.056
47DAP/reference	1.06863	0.44
52DAP/reference	0.91403	0.053
57DAP/reference	0.90758	0.027

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66903	0.011
17DAP/reference	0.71538	0.005
27DAP/reference	0.9526	0.393
39DAP/reference	1.03827	1
41DAP/reference	0.62844	0.011
42DAP/reference	0.88588	0.098
43DAP/reference	1.24122	0.308
47DAP/reference	1.39671	0.112
52DAP/reference	0.70116	0.003
57DAP/reference	1.04605	0.609

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90223	0.249
17DAP/reference	0.81331	0.159
27DAP/reference	0.92787	0.055
39DAP/reference	0.83469	0.122
41DAP/reference	0.96187	0.237
42DAP/reference	1.0615	0.566
43DAP/reference	1.13365	0.264
47DAP/reference	0.63556	0.005
52DAP/reference	0.81422	0.193
57DAP/reference	0.60236	0.021

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17357	1
26DAP/20DAP	0.78903	0.512
34DAP/26DAP	0.91365	0.777
51DAP/34DAP	1.0054	0.917
52DAP/51DAP	1.0437	0.86
53DAP/52DAP	0.92573	0.677
55DAP/53DAP	0.93432	0.632
57DAP/55DAP	1.13621	0.643
62DAP/57DAP	0.858	0.466
68DAP/62DAP	0.75855	0.152
68DAP/14DAP	0.67269	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	14.883	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	13.3154	0.058
Mature Green Tomato/Ripe Tomato	6.69422	0.166
Immature Eggplant/Mature Eggplant	13.3146	0.05
Ripe Pepper/Ripe Tomato	0.32577	0.224
Mature Eggplant/Ripe Tomato	1.47994	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.78193
1-1-2/M82	1.45352	1
12-2/M82	1.08342
12-4/M82	0.80787	0.319
1-3/M82	N/A	N/A
2-1-1/M82	0.87485	0.465
2-1/M82	0.62604
2-6/M82	1.00667
3-2/M82	N/A	N/A
4-1-1/M82	2.12068
4-1/M82	0.7619
4-3-2/M82	2.67235
4-3/M82	2.24094	0.268
5-3/M82	1.11327	1
6-2/M82	2.7596	0.235
6-3/M82	1.61006
7-1/M82	N/A	N/A
7-2/M82	0.92925	0.881
9-3-2/M82	0.8257

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.75615	0.348
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.09496	0.362
IL12-4/WTpooled	1.01531	1
IL1-4/WTpooled	0.8716	0.457
WT/WTpooled	0.94914	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	1.05845	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.17374	0.894
DC3000/delta hrp 6h	1.009	1
DC3000/delta hrp 12h	1.42633	1
DC3000/delta hrp 24h	0.88742	0.319

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.73764	0.042
DC3000 delta B/DC3000 delta AB	2.12528	0.035

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20194	0.254
Exp 36h	1.36296	0.693
Exp 60h	1.42271	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96942	1
Var 0h	0.93752	1
Var 12h I row2-row1	0.92775	0.627
Var 12h NI row2-row1	0.96573	0.82
Var 36h I row2-row1	1.03173	1
Var 36h NI row2-row1	1.04279	1
Var 60h I row2-row1	1.02714	1
Var 60h NI row2-row1	0.99027	1
Time course 0hI-0hNI	1.046	0.867
Time course 12hI-12hNI	1.0312	0.803
Time course 36hI-36hNI	1.26576	0.035
Time course 60hI-60hNI	0.9837	0.646

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)	1.72335	0.612
transgenic ySAMdc/azygous control (breaker)	0.54035	0.251
transgenic ySAMdc/azygous control (red)	1.23662	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.82498	0.156

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.85188	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69158	1
Manapal/WT (break)	1.07947	1
Manapal/WT (red)	2.80652	0.137