Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.9.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.09291	0.904
27DAP/17DAP	1.03871	0.992
39DAP/27DAP	1.06804	1
41DAP/39DAP	1.07533	0.78
42DAP/41DAP	1.17115	0.926
43DAP/42DAP	0.9328	0.801
47DAP/43DAP	1.05664	0.873
52DAP/47DAP	1.16538	0.626
57DAP/52DAP	1.01118	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09654	0.587
17DAP/reference	1.00895	0.787
27DAP/reference	0.98795	0.668
39DAP/reference	0.97654	0.565
41DAP/reference	1.06748	0.187
42DAP/reference	1.07454	0.093
43DAP/reference	0.99598	0.882
47DAP/reference	0.97362	0.322
52DAP/reference	0.9316	0.202
57DAP/reference	0.85215	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.93604	0.245
27DAP/17DAP	1.04129	0.905
39DAP/27DAP	1.04036	0.615
41DAP/39DAP	1.01164	0.896
42DAP/41DAP	1.0356	0.824
43DAP/42DAP	1.04645	0.382
47DAP/43DAP	1.00219	0.973
52DAP/47DAP	0.97762	0.925
57DAP/52DAP	0.97253	0.622
57DAP/7DAP	1.02463	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09453	0.325
17DAP/reference	1.33254	0.028
27DAP/reference	1.34128	0.03
39DAP/reference	1.61431	0.09
41DAP/reference	1.40563	0.027
42DAP/reference	1.76238	0.009
43DAP/reference	1.95707	0.007
47DAP/reference	1.21447	0.386
52DAP/reference	1.57694	0.008
57DAP/reference	1.73074	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13473	0.038
17DAP/reference	1.1564	0.203
27DAP/reference	1.03901	0.822
39DAP/reference	1.03688	1
41DAP/reference	1.09159	0.831
42DAP/reference	0.90961	0.169
43DAP/reference	1.09322	0.479
47DAP/reference	0.88663	0.016
52DAP/reference	1.09629	0.053
57DAP/reference	1.20839	0.083

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32185	0.158
17DAP/reference	1.16598	0.398
27DAP/reference	1.41174	0.042
39DAP/reference	1.52409	0.011
41DAP/reference	1.24821	0.156
42DAP/reference	1.11971	0.576
43DAP/reference	1.33732	0.19
47DAP/reference	0.99239	0.646
52DAP/reference	1.21918	0.153
57DAP/reference	0.72946	0.036

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96514	1
26DAP/20DAP	1.0083	1
34DAP/26DAP	0.91544	0.214
51DAP/34DAP	0.96925	0.737
52DAP/51DAP	1.04841	0.588
53DAP/52DAP	1.06281
55DAP/53DAP	1.10852	0.712
57DAP/55DAP	0.92946	0.638
62DAP/57DAP	1.05082	0.902
68DAP/62DAP	0.8847	0.345
68DAP/14DAP	0.94709	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.12518	0.092

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.15389	0.113
Mature Green Tomato/Ripe Tomato	1.33071	0.058
Immature Eggplant/Mature Eggplant	1.26587	0.051
Ripe Pepper/Ripe Tomato	1.27873	1
Mature Eggplant/Ripe Tomato	0.95288	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95056	0.907
1-1-2/M82	0.94713	0.958
12-2/M82	1.19686	1
12-4/M82	1.02093	1
1-3/M82	0.85355	0.501
2-1-1/M82	1.53081
2-1/M82	N/A	N/A
2-6/M82	1.08921	0.695
3-2/M82	1.07682
4-1-1/M82	0.92458
4-1/M82	1.00625
4-3-2/M82	0.92836	0.698
4-3/M82	1.07283
5-3/M82	1.06952	1
6-2/M82	1.20377
6-3/M82	1.02844
7-1/M82	0.93915	0.803
7-2/M82	0.9718	1
9-3-2/M82	0.93353	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.09028	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.75427	0.31
IL12-4/WTpooled	0.87551	0.71
IL1-4/WTpooled	0.82302
WT/WTpooled	0.97401	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	0.83643	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.9998	1
DC3000/delta hrp 6h	0.93777	0.95
DC3000/delta hrp 12h	0.93091	1
DC3000/delta hrp 24h	1.07705	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.26217	0.042
DC3000 delta B/DC3000 delta AB	1.19867	0.208

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00608	1
Exp 36h	1.4809	0.489
Exp 60h	1.3441	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99369	1
Var 0h	0.9599	1
Var 12h I row2-row1	1.28821	0.254
Var 12h NI row2-row1	0.99469	1
Var 36h I row2-row1	0.98716	1
Var 36h NI row2-row1	0.87332	0.329
Var 60h I row2-row1	0.9994	1
Var 60h NI row2-row1	1.07548	0.904
Time course 0hI-0hNI	1.03283	0.833
Time course 12hI-12hNI	1.05788	0.512
Time course 36hI-36hNI	1.16971	0.031
Time course 60hI-60hNI	1.69247	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)	1.31923	0.222
transgenic ySAMdc/azygous control (breaker)	0.66749	0.139
transgenic ySAMdc/azygous control (red)	0.98399	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05321	0.066

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02654	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.66759	0.172
Manapal/WT (break)	0.98763	1
Manapal/WT (red)	1.20384	0.142