Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.15.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73933	0.159
27DAP/17DAP	0.94611	0.853
39DAP/27DAP	0.95696	0.67
41DAP/39DAP	0.98077	0.902
42DAP/41DAP	1.04276	1
43DAP/42DAP	0.86539	0.744
47DAP/43DAP	1.09275	0.842
52DAP/47DAP	1.09426	0.794
57DAP/52DAP	1.09939	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.00234	0.009
17DAP/reference	1.38071	0.012
27DAP/reference	1.03622	0.569
39DAP/reference	1.12823	0.075
41DAP/reference	1.29667	0.018
42DAP/reference	1.10175	0.287
43DAP/reference	1.30439	0.089
47DAP/reference	0.99822	0.602
52DAP/reference	0.86354	0.042
57DAP/reference	0.82924	0.039

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.71732	0.121
27DAP/17DAP	1.09593	0.754
39DAP/27DAP	0.93635	0.622
41DAP/39DAP	0.98163	0.997
42DAP/41DAP	1.02417	1
43DAP/42DAP	1.20658	0.192
47DAP/43DAP	1.3553	0.914
52DAP/47DAP	1.4102	0.192
57DAP/52DAP	1.34415	0.344
57DAP/7DAP	0.79912	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.4199	0.025
17DAP/reference	0.85254	0.338
27DAP/reference	0.83911	0.076
39DAP/reference	0.91991	0.354
41DAP/reference	0.69048	0.023
42DAP/reference	0.77212	0.038
43DAP/reference	1.02733	0.974
47DAP/reference	0.84856	0.222
52DAP/reference	0.70858	0.017
57DAP/reference	0.81212	0.012

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40242	0.029
17DAP/reference	1.07954	0.839
27DAP/reference	1.13349	0.352
39DAP/reference	0.90651	0.11
41DAP/reference	1.06119	0.893
42DAP/reference	1.09171	0.509
43DAP/reference	1.41944	0.164
47DAP/reference	1.21356	0.036
52DAP/reference	1.13387	0.079
57DAP/reference	1.15986	0.672

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68354	0.032
17DAP/reference	1.14329	0.037
27DAP/reference	0.93252	0.357
39DAP/reference	0.99349	0.591
41DAP/reference	0.9247	0.264
42DAP/reference	0.97105	0.552
43DAP/reference	1.02996	0.796
47DAP/reference	1.14283	0.355
52DAP/reference	0.79523	0.193
57DAP/reference	1.0088	0.633

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.7315	0.966
26DAP/20DAP	0.91624	0.512
34DAP/26DAP	1.41752	0.542
51DAP/34DAP	0.89812	0.64
52DAP/51DAP	1.34277	0.186
53DAP/52DAP	1.11771	0.768
55DAP/53DAP	1.28242	0.589
57DAP/55DAP	1.37648	0.666
62DAP/57DAP	0.82401	0.088
68DAP/62DAP	1.04147	0.885
68DAP/14DAP	0.58457	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.80924	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.54275	0.179
Mature Green Tomato/Ripe Tomato	1.48106
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.65798
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
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	0.99833
IL2-6/WTpooled	2.91325
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	1.03901	0.525
IL1-4/WTpooled	0.82137	0.834
WT/WTpooled	1.16057	0.89

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	0.77327	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97941	1
DC3000/delta hrp 6h	1.12083	0.95
DC3000/delta hrp 12h	1.01831	1
DC3000/delta hrp 24h	0.92308	0.585

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.34966
DC3000 delta B/DC3000 delta AB	0.82519	0.27

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97892	1
Exp 36h	N/A	N/A
Exp 60h	1.03891	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.13575	1
Var 0h	0.8809	0.933
Var 12h I row2-row1	0.92117	0.353
Var 12h NI row2-row1	1.0567	0.649
Var 36h I row2-row1	1.50885	0.908
Var 36h NI row2-row1	0.90476	0.478
Var 60h I row2-row1	0.94639	0.952
Var 60h NI row2-row1	0.68329	0.932
Time course 0hI-0hNI	0.99409	1
Time course 12hI-12hNI	0.98236	0.886
Time course 36hI-36hNI	0.87117	0.07
Time course 60hI-60hNI	0.7547	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)	1.00146	1
transgenic ySAMdc/azygous control (breaker)	1.10813	0.248
transgenic ySAMdc/azygous control (red)	1.02898	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02476	0.261

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.0001	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13061	1
Manapal/WT (break)	0.91297	1
Manapal/WT (red)	N/A	N/A