Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.17.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.82538	0.106
27DAP/17DAP	0.56443	0.04
39DAP/27DAP	1.36647	0.358
41DAP/39DAP	1.02588	0.941
42DAP/41DAP	1.80615	0.295
43DAP/42DAP	1.24611	1
47DAP/43DAP	0.98435	0.804
52DAP/47DAP	0.499	0.078
57DAP/52DAP	1.39667	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.76162	0.014
17DAP/reference	1.30329	0.138
27DAP/reference	0.97023	0.642
39DAP/reference	1.46549	0.072
41DAP/reference	1.36973	0.058
42DAP/reference	1.84047	0.001
43DAP/reference	1.78485	0.007
47DAP/reference	1.9141	0.006
52DAP/reference	0.99634	0.654
57DAP/reference	0.86525	0.082

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9561	0.629
27DAP/17DAP	1.2842	0.518
39DAP/27DAP	0.74338	0.167
41DAP/39DAP	2.0547	0.579
42DAP/41DAP	1.15322	0.999
43DAP/42DAP	1.32763	0.23
47DAP/43DAP	1.20192	0.54
52DAP/47DAP	1.86987	0.074
57DAP/52DAP	0.53882	0.052
57DAP/7DAP	1.36908	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93318	0.326
17DAP/reference	0.8908	0.192
27DAP/reference	0.98595	0.614
39DAP/reference	0.75372	0.039
41DAP/reference	1.03389	0.709
42DAP/reference	0.89043	0.111
43DAP/reference	0.86919	0.047
47DAP/reference	1.19116	0.458
52DAP/reference	0.98743	0.679
57DAP/reference	0.89871	0.132

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33999	0.319
17DAP/reference	1.71263	0.107
27DAP/reference	1.37538	0.239
39DAP/reference	0.91817	0.208
41DAP/reference	1.50343	0.047
42DAP/reference	1.28278	0.166
43DAP/reference	1.32359	0.075
47DAP/reference	1.53227	0.01
52DAP/reference	1.04566	1
57DAP/reference	1.21337	0.654

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95637	0.489
17DAP/reference	0.9865	0.739
27DAP/reference	0.87044	0.092
39DAP/reference	0.92697	0.271
41DAP/reference	0.97294	0.618
42DAP/reference	1.49013	0.214
43DAP/reference	2.04565	0.229
47DAP/reference	2.20271	0.007
52DAP/reference	1.08716	0.694
57DAP/reference	1.17827	0.419

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80215	1
26DAP/20DAP	1.04944	1
34DAP/26DAP	1.20046	0.819
51DAP/34DAP	1.42682	0.524
52DAP/51DAP	1.09802	0.836
53DAP/52DAP	0.90446	0.758
55DAP/53DAP	1.25156	0.046
57DAP/55DAP	0.70705	0.09
62DAP/57DAP	1.15524	0.902
68DAP/62DAP	0.83583	0.668
68DAP/14DAP	0.96757

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	70.1242	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	1.15981	0.752
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	1.23541
Mature Eggplant/Ripe Tomato	1.12767	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.06395	0.877
1-1-2/M82	1.17354
12-2/M82	N/A	N/A
12-4/M82	2.19348	1
1-3/M82	N/A	N/A
2-1-1/M82	1.19869
2-1/M82	N/A	N/A
2-6/M82	1.38399
3-2/M82	1.02887
4-1-1/M82	N/A	N/A
4-1/M82	7.15893	1
4-3-2/M82	1.53792	0.508
4-3/M82	1.12334
5-3/M82	1.20666	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.11157
9-3-2/M82	2.6344

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.84719
IL2-6/WTpooled	0.96632	1
IL7-5/WTpooled	0.98804
IL7-3/WTpooled	0.79	0.294
IL12-4/WTpooled	0.97371	1
IL1-4/WTpooled	0.82968	0.699
WT/WTpooled	1.15896	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	0.92618	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87649	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.03233	1
DC3000/delta hrp 24h	1.04042	0.779

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.22242
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	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0124	1
Var 0h	0.39865	0.291
Var 12h I row2-row1	0.99593	1
Var 12h NI row2-row1	0.79875	0.488
Var 36h I row2-row1	0.83265	1
Var 36h NI row2-row1	1.12447	1
Var 60h I row2-row1	1.29153	0.562
Var 60h NI row2-row1	1.20805	0.904
Time course 0hI-0hNI	1.04079	0.764
Time course 12hI-12hNI	1.05693	0.741
Time course 36hI-36hNI	0.99703	0.768
Time course 60hI-60hNI	1.01585	0.575

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.95212	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.42427	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88764	1
Manapal/WT (break)	0.81769	1
Manapal/WT (red)	0.78387	0.503