Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.11.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71639	0.111
27DAP/17DAP	1.66216	0.261
39DAP/27DAP	1.36986	0.225
41DAP/39DAP	0.974	0.879
42DAP/41DAP	1.34178	0.556
43DAP/42DAP	1.00467	0.937
47DAP/43DAP	1.13669	0.52
52DAP/47DAP	1.03164	0.953
57DAP/52DAP	1.27442	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9097	0.262
17DAP/reference	0.97977	0.701
27DAP/reference	0.91495	0.208
39DAP/reference	1.07908	0.486
41DAP/reference	1.02033	1
42DAP/reference	0.91875	0.115
43DAP/reference	1.07353	0.403
47DAP/reference	0.94569	0.279
52DAP/reference	0.88455	0.189
57DAP/reference	0.88297	0.047

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9742	0.763
27DAP/17DAP	1.05514	0.831
39DAP/27DAP	1.17981	0.245
41DAP/39DAP	0.92808	0.764
42DAP/41DAP	1.46809	0.234
43DAP/42DAP	0.87153	0.256
47DAP/43DAP	4.15032	0.664
52DAP/47DAP	0.83167	0.316
57DAP/52DAP	1.02355	0.887
57DAP/7DAP	0.52828

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18081	0.083
17DAP/reference	1.36524	0.018
27DAP/reference	1.11218	0.664
39DAP/reference	1.41663	0.166
41DAP/reference	1.36827	0.021
42DAP/reference	1.19337	0.059
43DAP/reference	1.564	0.034
47DAP/reference	0.92254	0.671
52DAP/reference	1.04754	0.886
57DAP/reference	1.24052	0.087

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09721	0.569
17DAP/reference	0.93241	0.499
27DAP/reference	0.84589	0.09
39DAP/reference	0.78974	0.074
41DAP/reference	0.82793	0.085
42DAP/reference	0.87428	0.261
43DAP/reference	1.05865	0.939
47DAP/reference	1.1565	0.061
52DAP/reference	1.26319	0.838
57DAP/reference	1.05342	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09254	0.827
17DAP/reference	1.14588	0.595
27DAP/reference	1.79287	0.014
39DAP/reference	1.42278	0.019
41DAP/reference	1.24676	0.018
42DAP/reference	1.17408	0.5
43DAP/reference	1.20571	0.84
47DAP/reference	0.9432	0.296
52DAP/reference	1.2596	0.153
57DAP/reference	1.09158	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.63611	0.966
26DAP/20DAP	1.17048	0.558
34DAP/26DAP	1.10053	1
51DAP/34DAP	2.34393	0.352
52DAP/51DAP	1.11951	0.358
53DAP/52DAP	1.20305	0.753
55DAP/53DAP	1.09161	0.748
57DAP/55DAP	1.02203	0.923
62DAP/57DAP	1.98131
68DAP/62DAP	1.06771	0.827
68DAP/14DAP	1.37826	0.223

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.49657	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.6891	0.107
Immature Eggplant/Mature Eggplant	3.22047	0.051
Ripe Pepper/Ripe Tomato	0.72555	0.224
Mature Eggplant/Ripe Tomato	0.77531	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.31799	0.43
1-1-2/M82	1.06065	0.977
12-2/M82	0.94955
12-4/M82	0.81316	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.80423	0.465
2-1/M82	1.04587	0.345
2-6/M82	0.90703	1
3-2/M82	1.15481
4-1-1/M82	1.00561
4-1/M82	0.90824	0.737
4-3-2/M82	1.00587	0.262
4-3/M82	0.99306	1
5-3/M82	1.10996	1
6-2/M82	1.02116
6-3/M82	1.00741	1
7-1/M82	1.07061	1
7-2/M82	1.26099	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.89288	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08802	1
IL12-4/WTpooled	1.06202	0.624
IL1-4/WTpooled	1.10262
WT/WTpooled	1.04097	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	1.16759	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.8825	0.868
DC3000/delta hrp 6h	0.97513	0.95
DC3000/delta hrp 12h	0.97392	1
DC3000/delta hrp 24h	1.72888	0.029

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.10493	0.598
DC3000 delta B/DC3000 delta AB	1.23506	0.284

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05234	1
Exp 36h	1.40921	0.349
Exp 60h	1.34344	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98433	1
Var 0h	0.98203	1
Var 12h I row2-row1	1.10143	0.235
Var 12h NI row2-row1	0.9017	0.82
Var 36h I row2-row1	1.08592	0.908
Var 36h NI row2-row1	0.89194	0.743
Var 60h I row2-row1	0.83025	0.293
Var 60h NI row2-row1	0.88409	0.866
Time course 0hI-0hNI	0.92464	0.269
Time course 12hI-12hNI	1.15491	0.162
Time course 36hI-36hNI	1.5693	0.005
Time course 60hI-60hNI	2.35395	0.008

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)	1.09589	0.511
transgenic ySAMdc/azygous control (breaker)	1.19109	0.248
transgenic ySAMdc/azygous control (red)	1.02125	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9286	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.84388	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.29488	0.105
Manapal/WT (break)	1.13433	0.381
Manapal/WT (red)	1.08053	1