Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.16.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93319	0.652
27DAP/17DAP	0.74408	0.227
39DAP/27DAP	1.23962	0.622
41DAP/39DAP	0.99762	0.944
42DAP/41DAP	1.05437	0.997
43DAP/42DAP	1.00174	0.937
47DAP/43DAP	1.03603	0.825
52DAP/47DAP	0.63301	0.195
57DAP/52DAP	2.02663	0.561

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.83122	0.007
17DAP/reference	1.10137	0.342
27DAP/reference	1.09585	0.648
39DAP/reference	1.02836	0.76
41DAP/reference	0.86551	0.154
42DAP/reference	0.77318	0.002
43DAP/reference	1.00475	1
47DAP/reference	1.40507	0.101
52DAP/reference	1.3347	0.019
57DAP/reference	1.31318	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.124	0.687
27DAP/17DAP	0.93977	0.821
39DAP/27DAP	0.8533	0.394
41DAP/39DAP	1.33112	0.455
42DAP/41DAP	1.12637	0.773
43DAP/42DAP	0.92765	0.482
47DAP/43DAP	1.06685	0.957
52DAP/47DAP	1.33808	0.266
57DAP/52DAP	1.21242	0.455
57DAP/7DAP	1.20517	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.53594	0.035
17DAP/reference	1.19826	0.162
27DAP/reference	0.9516	0.303
39DAP/reference	1.61659	0.007
41DAP/reference	0.86317	0.174
42DAP/reference	1.03521	1
43DAP/reference	1.43651	0.053
47DAP/reference	1.35579	0.272
52DAP/reference	1.69237	0.018
57DAP/reference	1.65555	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.39886	0.146
17DAP/reference	0.87878	0.07
27DAP/reference	0.75296	0.064
39DAP/reference	1.08315	0.477
41DAP/reference	1.02918	0.749
42DAP/reference	0.76101	0.046
43DAP/reference	0.91601	0.378
47DAP/reference	0.90817	0.168
52DAP/reference	0.78863	0.004
57DAP/reference	0.75562	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.95123	0.04
17DAP/reference	0.89006	0.322
27DAP/reference	0.96607	0.516
39DAP/reference	0.92835	0.222
41DAP/reference	0.9434	0.331
42DAP/reference	0.98933	0.816
43DAP/reference	1.15178	0.343
47DAP/reference	0.91748	0.296
52DAP/reference	0.83679	0.167
57DAP/reference	1.39038	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00545	1
26DAP/20DAP	0.89321	1
34DAP/26DAP	1.01552	1
51DAP/34DAP	1.17491	0.511
52DAP/51DAP	0.96506	1
53DAP/52DAP	0.98938	0.854
55DAP/53DAP	1.00261	0.784
57DAP/55DAP	0.86168	0.37
62DAP/57DAP	0.90143	0.871
68DAP/62DAP	1.08786	0.885
68DAP/14DAP	0.93003	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79383	0.115

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50684	0.117
Mature Green Tomato/Ripe Tomato	3.33275	0.032
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.13921	0.258
Mature Eggplant/Ripe Tomato	0.6818	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01735	1
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.87106	1
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	N/A	N/A
4-3/M82	1.10639
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.10034	1
IL12-4/WTpooled	1.45194	0.42
IL1-4/WTpooled	3.08138	0.426
WT/WTpooled	1.00954	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	1.02337	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02298	0.921
DC3000/delta hrp 6h	1.14753	0.777
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	0.64065	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.35396	0.441
DC3000 delta B/DC3000 delta AB	1.76554	0.437

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08199	1
Exp 36h	0.78303	0.504
Exp 60h	0.75401	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02423	1
Var 0h	1.25137	0.98
Var 12h I row2-row1	1.03292	0.544
Var 12h NI row2-row1	1.01239	1
Var 36h I row2-row1	0.85228	1
Var 36h NI row2-row1	1.21167	0.482
Var 60h I row2-row1	0.9956	1
Var 60h NI row2-row1	1.08782	1
Time course 0hI-0hNI	0.93873	0.631
Time course 12hI-12hNI	0.9042	0.179
Time course 36hI-36hNI	0.7853	0.024
Time course 60hI-60hNI	0.30425	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)	1.09311	0.408
transgenic ySAMdc/azygous control (breaker)	1.27692	0.248
transgenic ySAMdc/azygous control (red)	1.04173	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03846	0.1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.99587	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.24335	0.083
Manapal/WT (break)	1.726	0.183
Manapal/WT (red)	1.53065	0.164