Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.20.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98179	0.858
27DAP/17DAP	1.25648	0.849
39DAP/27DAP	0.9709	0.733
41DAP/39DAP	1.09226	0.938
42DAP/41DAP	1.10929	1
43DAP/42DAP	1.34658	0.867
47DAP/43DAP	1.0816	0.926
52DAP/47DAP	1.23461	0.641
57DAP/52DAP	0.98674	0.978

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31283	0.241
17DAP/reference	1.51719	0.122
27DAP/reference	1.48425	0.02
39DAP/reference	1.20193
41DAP/reference	2.08649	0.085
42DAP/reference	0.98334	0.384
43DAP/reference	0.3587
47DAP/reference	1.01442	1
52DAP/reference	0.51383
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.5656	0.038
27DAP/17DAP	0.94135	0.782
39DAP/27DAP	1.07341	0.718
41DAP/39DAP	1.251	0.484
42DAP/41DAP	0.90307	0.35
43DAP/42DAP	1.15201	0.079
47DAP/43DAP	1.21825	0.833
52DAP/47DAP	1.16002	0.689
57DAP/52DAP	1.80393	0.249
57DAP/7DAP	1.21988	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94623	0.246
17DAP/reference	0.95366	0.253
27DAP/reference	1.13959	0.088
39DAP/reference	0.84345	0.043
41DAP/reference	0.96359	0.311
42DAP/reference	1.22206	0.018
43DAP/reference	1.16066	0.028
47DAP/reference	1.09543	0.67
52DAP/reference	1.60145	0.007
57DAP/reference	1.30481	0.066

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12828	0.823
17DAP/reference	0.99081	0.728
27DAP/reference	0.95601	0.452
39DAP/reference	1.03925	1
41DAP/reference	1.04796	0.672
42DAP/reference	1.16705	0.254
43DAP/reference	1.59024	0.082
47DAP/reference	1.13941	0.232
52DAP/reference	1.19042	0.145
57DAP/reference	1.28313	0.011

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94702	0.362
17DAP/reference	1.00553	0.87
27DAP/reference	0.89423	0.108
39DAP/reference	1.10288	0.081
41DAP/reference	1.21546	0.096
42DAP/reference	1.18994	0.111
43DAP/reference	0.94922	0.468
47DAP/reference	1.11209	0.179
52DAP/reference	1.27679	0.212
57DAP/reference	1.07565	0.673

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05523	0.966
26DAP/20DAP	1.47919	1
34DAP/26DAP	1.32455	0.542
51DAP/34DAP	1.36573	0.261
52DAP/51DAP	1.17914	0.481
53DAP/52DAP	1.20572	0.23
55DAP/53DAP	1.032	0.989
57DAP/55DAP	0.90241	0.664
62DAP/57DAP	0.89197	0.681
68DAP/62DAP	3.26113	0.013
68DAP/14DAP	3.52345	0.017

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.51658	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.70703	0.478
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.29169
Mature Eggplant/Ripe Tomato	0.26821	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.62123	0.883
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.82103	1
1-3/M82	1.083	1
2-1-1/M82	1.28173	1
2-1/M82	1.03921	1
2-6/M82	1.35673	1
3-2/M82	N/A	N/A
4-1-1/M82	1.18024
4-1/M82	0.54289
4-3-2/M82	N/A	N/A
4-3/M82	0.81407
5-3/M82	1.52941	1
6-2/M82	N/A	N/A
6-3/M82	2.24654
7-1/M82	N/A	N/A
7-2/M82	1.06235	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.88842	0.243
IL2-6/WTpooled	1.00292	1
IL7-5/WTpooled	1.07862	0.792
IL7-3/WTpooled	0.84751	0.418
IL12-4/WTpooled	0.84256	0.71
IL1-4/WTpooled	0.95857	0.834
WT/WTpooled	1.1507	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	1.7318	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03286	0.921
DC3000/delta hrp 6h	1.12571	1
DC3000/delta hrp 12h	0.87009	1
DC3000/delta hrp 24h	1.47679	0.027

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06952	0.515
DC3000 delta B/DC3000 delta AB	0.91808	0.483

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11689	1
Exp 36h	1.10813	1
Exp 60h	0.65659	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02309	1
Var 0h	N/A	N/A
Var 12h I row2-row1	3.30372	0.242
Var 12h NI row2-row1	1.42295	0.281
Var 36h I row2-row1	0.85101	1
Var 36h NI row2-row1	1.15609	1
Var 60h I row2-row1	0.5892	0.292
Var 60h NI row2-row1	1.36436	0.793
Time course 0hI-0hNI	1.05467	0.852
Time course 12hI-12hNI	1.08309	0.724
Time course 36hI-36hNI	0.75549	0.023
Time course 60hI-60hNI	1.61517	0.115

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)	1.16397	0.232
transgenic ySAMdc/azygous control (breaker)	0.76887	0.15
transgenic ySAMdc/azygous control (red)	0.93963	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	1.13382	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.06292	1
Manapal/WT (break)	1.58175	0.123
Manapal/WT (red)	0.76095	0.181