Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.4.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93914	0.558
27DAP/17DAP	1.02598	0.916
39DAP/27DAP	0.98932	0.782
41DAP/39DAP	1.65751	0.376
42DAP/41DAP	0.93205	1
43DAP/42DAP	1.11869	0.823
47DAP/43DAP	1.02331	0.979
52DAP/47DAP	1.22984	0.521
57DAP/52DAP	0.98338	0.974

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0054	1
17DAP/reference	1.04633	0.053
27DAP/reference	1.03705	0.306
39DAP/reference	1.04659	0.229
41DAP/reference	1.0336	0.393
42DAP/reference	1.00305	1
43DAP/reference	1.01338	0.758
47DAP/reference	1.0173	0.773
52DAP/reference	0.98016	0.546
57DAP/reference	1.07958	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97599	0.663
27DAP/17DAP	1.01189	0.969
39DAP/27DAP	1.0753	0.499
41DAP/39DAP	1.05267	0.79
42DAP/41DAP	1.03105	0.886
43DAP/42DAP	0.96049	0.447
47DAP/43DAP	1.00025	1
52DAP/47DAP	1.00908	0.979
57DAP/52DAP	1.0026	1
57DAP/7DAP	1.13838	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97719	0.326
17DAP/reference	0.93638	0.056
27DAP/reference	0.90698	0.01
39DAP/reference	0.97489	0.17
41DAP/reference	1.0191	0.836
42DAP/reference	0.9746	0.371
43DAP/reference	0.99626	0.694
47DAP/reference	0.9945	1
52DAP/reference	1.01148	0.941
57DAP/reference	0.99082	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22359	0.373
17DAP/reference	1.05001	0.264
27DAP/reference	0.92432	0.317
39DAP/reference	1.00724	1
41DAP/reference	0.92658	0.262
42DAP/reference	0.82843	0.032
43DAP/reference	0.96739	0.459
47DAP/reference	0.91704	0.102
52DAP/reference	1.05796	0.114
57DAP/reference	1.01408	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90758	0.059
17DAP/reference	0.96467	0.426
27DAP/reference	0.91623	0.047
39DAP/reference	0.90691	0.016
41DAP/reference	0.90836	0.148
42DAP/reference	0.8547	0.025
43DAP/reference	0.91332	0.025
47DAP/reference	0.96836	0.409
52DAP/reference	0.90416	0.242
57DAP/reference	0.84863	0.022

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96221	1
26DAP/20DAP	0.97389	1
34DAP/26DAP	0.98711	1
51DAP/34DAP	1.00466	1
52DAP/51DAP	0.99228	1
53DAP/52DAP	0.81271	0.179
55DAP/53DAP	0.93481	0.761
57DAP/55DAP	1.0157	0.961
62DAP/57DAP	0.99368	1
68DAP/62DAP	0.94467	0.787
68DAP/14DAP	0.78559	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.03953	0.821

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.34734	0.063
Mature Green Tomato/Ripe Tomato	1.03535	0.898
Immature Eggplant/Mature Eggplant	1.03489	0.683
Ripe Pepper/Ripe Tomato	4.37019	1
Mature Eggplant/Ripe Tomato	4.75906	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03431	1
1-1-2/M82	1.02048	1
12-2/M82	1.05659
12-4/M82	0.94579	1
1-3/M82	0.9844	1
2-1-1/M82	0.97495	1
2-1/M82	0.96461
2-6/M82	0.98377	1
3-2/M82	1.02877	1
4-1-1/M82	0.97848	1
4-1/M82	0.82961
4-3-2/M82	1.02379	1
4-3/M82	0.93593	0.72
5-3/M82	1.03438	1
6-2/M82	1.05236	1
6-3/M82	0.99258	1
7-1/M82	0.95739	1
7-2/M82	1.02658	0.385
9-3-2/M82	1.05481	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.69406	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.17553	1
IL12-4/WTpooled	0.96131	1
IL1-4/WTpooled	0.98781
WT/WTpooled	0.95772	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	1.39936	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05747	0.921
DC3000/delta hrp 6h	1.35797	1
DC3000/delta hrp 12h	0.95637	1
DC3000/delta hrp 24h	1.08368	0.308

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.20699	0.042
DC3000 delta B/DC3000 delta AB	1.19063	0.217

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17965	1
Exp 36h	1.35763	0.693
Exp 60h	1.7516	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.00971	1
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.76655	0.246
transgenic ySAMdc/azygous control (breaker)	1.22081	1
transgenic ySAMdc/azygous control (red)	1.03314	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95388	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05267	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.16501	0.096
Manapal/WT (break)	0.77778	0.299
Manapal/WT (red)	0.83775	0.36