Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.15.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32354	0.681
27DAP/17DAP	1.07923	0.911
39DAP/27DAP	1.03282	0.899
41DAP/39DAP	1.0603	0.85
42DAP/41DAP	1.16498	0.752
43DAP/42DAP	1.20474	0.553
47DAP/43DAP	0.87111	0.584
52DAP/47DAP	1.0433	0.982
57DAP/52DAP	1.0248	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01812	1
17DAP/reference	0.95534	0.474
27DAP/reference	0.99794	0.822
39DAP/reference	0.92785	0.333
41DAP/reference	1.01684	0.963
42DAP/reference	0.90026	0.107
43DAP/reference	0.931	0.429
47DAP/reference	0.9289	0.161
52DAP/reference	1.02303	1
57DAP/reference	0.93157	0.248

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25548	0.319
27DAP/17DAP	0.89004	0.684
39DAP/27DAP	1.31108	0.117
41DAP/39DAP	0.95953	0.934
42DAP/41DAP	1.34964	0.042
43DAP/42DAP	0.92283	0.538
47DAP/43DAP	0.94765	0.823
52DAP/47DAP	0.85707	0.77
57DAP/52DAP	0.85937	0.551
57DAP/7DAP	0.84149	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8701	0.146
17DAP/reference	0.80298	0.013
27DAP/reference	0.93637	0.248
39DAP/reference	0.93555	0.307
41DAP/reference	0.90529	0.259
42DAP/reference	0.8968	0.16
43DAP/reference	0.85364	0.069
47DAP/reference	0.9117	0.222
52DAP/reference	0.87055	0.179
57DAP/reference	0.87581	0.176

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02357	0.786
17DAP/reference	1.0062	1
27DAP/reference	1.04745	0.798
39DAP/reference	1.06986	1
41DAP/reference	1.09847	0.944
42DAP/reference	0.98203	0.534
43DAP/reference	1.29273	0.272
47DAP/reference	0.9497	0.246
52DAP/reference	0.9715	0.469
57DAP/reference	0.7894	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90788	0.268
17DAP/reference	1.144	0.887
27DAP/reference	0.7915	0.041
39DAP/reference	0.88294	0.092
41DAP/reference	0.87171	0.185
42DAP/reference	0.90651	0.361
43DAP/reference	1.02618	0.614
47DAP/reference	1.04108	1
52DAP/reference	0.81281	0.174
57DAP/reference	1.17428	0.522

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96524	1
26DAP/20DAP	0.67954	0.112
34DAP/26DAP	1.313	1
51DAP/34DAP	1.53877	0.795
52DAP/51DAP	0.95069	1
53DAP/52DAP	0.72795	0.25
55DAP/53DAP	0.75548	0.417
57DAP/55DAP	0.8804	0.59
62DAP/57DAP	1.02803	0.994
68DAP/62DAP	1.39714	0.036
68DAP/14DAP	0.30428

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98024	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.75831	0.106
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.15285
Mature Eggplant/Ripe Tomato	0.13319	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.97084
12-2/M82	0.92674
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
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	N/A	N/A
4-3-2/M82	0.70826
4-3/M82	1.06588	1
5-3/M82	1.06148
6-2/M82	N/A	N/A
6-3/M82	1.01698	1
7-1/M82	N/A	N/A
7-2/M82	0.90458
9-3-2/M82	0.69306

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.51162	0.243
IL2-6/WTpooled	0.96315	1
IL7-5/WTpooled	1.50819	0.792
IL7-3/WTpooled	0.80965	0.31
IL12-4/WTpooled	0.87762	0.543
IL1-4/WTpooled	0.93998	0.834
WT/WTpooled	0.90548	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	0.90872	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.85232	0.849
DC3000/delta hrp 6h	1.00569	0.95
DC3000/delta hrp 12h	1.04573	1
DC3000/delta hrp 24h	0.95936

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	1.04898	1
Exp 36h	0.42177	0.171
Exp 60h	0.72734	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97061	1
Var 0h	1.13453	0.782
Var 12h I row2-row1	7.5245	0.544
Var 12h NI row2-row1	0.64587	0.82
Var 36h I row2-row1	0.95214	1
Var 36h NI row2-row1	1.2033	0.482
Var 60h I row2-row1	1.04153	1
Var 60h NI row2-row1	1.02641	0.904
Time course 0hI-0hNI	0.87111	1
Time course 12hI-12hNI	1.10634	0.747
Time course 36hI-36hNI	1.00186	0.857
Time course 60hI-60hNI	0.74711	0.081

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)	1.07742	0.654
transgenic ySAMdc/azygous control (breaker)	1.17895	0.248
transgenic ySAMdc/azygous control (red)	0.88378	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90418	0.054

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.60109	0.233

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.01873	0.096
Manapal/WT (break)	2.12843	0.126
Manapal/WT (red)	1.18233	1