Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.2.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.88257	0.389
27DAP/17DAP	1.17136	0.833
39DAP/27DAP	1.01174	0.749
41DAP/39DAP	1.19091	0.777
42DAP/41DAP	1.33395	0.619
43DAP/42DAP	0.91168	0.671
47DAP/43DAP	1.1422	0.873
52DAP/47DAP	1.08336	0.987
57DAP/52DAP	1.40726	0.89

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91415	0.101
17DAP/reference	0.71903	0.007
27DAP/reference	0.92273	0.265
39DAP/reference	0.90083	0.025
41DAP/reference	0.76757	0.009
42DAP/reference	1.00352	0.755
43DAP/reference	0.93768	0.273
47DAP/reference	1.00077	0.764
52DAP/reference	1.08397	0.951
57DAP/reference	1.1922	0.018

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14678	0.445
27DAP/17DAP	0.99468	0.919
39DAP/27DAP	0.91984	0.419
41DAP/39DAP	0.98079	0.986
42DAP/41DAP	0.93992	0.607
43DAP/42DAP	0.97675	0.774
47DAP/43DAP	0.92422	0.489
52DAP/47DAP	0.8279	0.28
57DAP/52DAP	0.86341	0.391
57DAP/7DAP	1.72581	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12041	0.776
17DAP/reference	1.4542	0.754
27DAP/reference	1.61655	0.197
39DAP/reference	1.68411	0.009
41DAP/reference	1.11235	0.223
42DAP/reference	1.20613	0.132
43DAP/reference	0.96841	0.459
47DAP/reference	0.92178	0.293
52DAP/reference	0.82466	0.254
57DAP/reference	1.10946	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8931	0.329
17DAP/reference	0.80971	0.008
27DAP/reference	0.97306	0.519
39DAP/reference	0.98392	0.509
41DAP/reference	1.05157	0.72
42DAP/reference	1.04533	0.879
43DAP/reference	0.93778	0.385
47DAP/reference	0.87351	0.015
52DAP/reference	0.98183	0.5
57DAP/reference	0.99751	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70459	0.147
17DAP/reference	0.88774	0.56
27DAP/reference	0.94219
39DAP/reference	1.04764	0.752
41DAP/reference	0.7909	0.459
42DAP/reference	1.24633	0.063
43DAP/reference	1.31664	0.087
47DAP/reference	0.93519	0.269
52DAP/reference	1.00888	0.928
57DAP/reference	1.25963	0.052

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	8.40319	0.966
26DAP/20DAP	0.9083	1
34DAP/26DAP	1.38624	0.819
51DAP/34DAP	1.01526	0.925
52DAP/51DAP	0.80793	1
53DAP/52DAP	0.99445	0.917
55DAP/53DAP	1.14965	0.981
57DAP/55DAP	1.61151	0.364
62DAP/57DAP	0.88353	0.871
68DAP/62DAP	1.14704	0.682
68DAP/14DAP	1.17593	0.346

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84773	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52319	0.12
Mature Green Tomato/Ripe Tomato	1.942	0.04
Immature Eggplant/Mature Eggplant	0.93	0.448
Ripe Pepper/Ripe Tomato	1.27449	1
Mature Eggplant/Ripe Tomato	1.05405	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3718	0.526
1-1-2/M82	1.09403	1
12-2/M82	1.33836
12-4/M82	0.8763	0.33
1-3/M82	1.27598
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.06695	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.31301
4-3-2/M82	N/A	N/A
4-3/M82	1.09146	1
5-3/M82	1.02798	1
6-2/M82	N/A	N/A
6-3/M82	1.0442
7-1/M82	N/A	N/A
7-2/M82	0.96173
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.94447	1
IL2-6/WTpooled	0.29787
IL7-5/WTpooled	1.22778	1
IL7-3/WTpooled	1.01707	1
IL12-4/WTpooled	0.79546	0.52
IL1-4/WTpooled	1.03819	1
WT/WTpooled	1.07528

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	0.93999	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97897	1
DC3000/delta hrp 6h	0.99217	0.95
DC3000/delta hrp 12h	0.88281	1
DC3000/delta hrp 24h	0.92267	0.782

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	0.60687

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86831	1
Exp 36h	1.01481	1
Exp 60h	0.90762	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93592	1
Var 0h	1.03588	1
Var 12h I row2-row1	1.07948	0.544
Var 12h NI row2-row1	0.98136	0.906
Var 36h I row2-row1	0.70479	0.805
Var 36h NI row2-row1	2.69475	1
Var 60h I row2-row1	0.94567	0.582
Var 60h NI row2-row1	1.57975	0.904
Time course 0hI-0hNI	0.96643	0.863
Time course 12hI-12hNI	0.97965	0.855
Time course 36hI-36hNI	0.76291	0.023
Time course 60hI-60hNI	0.49689	0.007

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)	1.0011	1
transgenic ySAMdc/azygous control (breaker)	1.11981	0.248
transgenic ySAMdc/azygous control (red)	1.01253	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96222	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.48187	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.77532	0.083
Manapal/WT (break)	1.82681	0.123
Manapal/WT (red)	3.31888	0.133