Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.8.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.7342	0.272
27DAP/17DAP	1.22313	0.873
39DAP/27DAP	1.02787	1
41DAP/39DAP	0.79759	0.276
42DAP/41DAP	0.83437	0.774
43DAP/42DAP	1.11725	1
47DAP/43DAP	0.86467	0.568
52DAP/47DAP	1.13872	0.754
57DAP/52DAP	1.02374	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1854	0.366
17DAP/reference	0.96968	0.597
27DAP/reference	1.11505	0.306
39DAP/reference	1.07172	0.413
41DAP/reference	1.01215	1
42DAP/reference	0.96355	0.287
43DAP/reference	0.91243	0.191
47DAP/reference	0.87113	0.025
52DAP/reference	1.00589	0.73
57DAP/reference	1.04235	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97305	0.732
27DAP/17DAP	1.48519	0.573
39DAP/27DAP	1.08701	0.565
41DAP/39DAP	0.94525	0.875
42DAP/41DAP	1.17102	0.273
43DAP/42DAP	1.00806	1
47DAP/43DAP	0.99258	0.971
52DAP/47DAP	1.1454	0.681
57DAP/52DAP	1.07747	0.703
57DAP/7DAP	1.6854	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69237	0.025
17DAP/reference	2.15007	0.007
27DAP/reference	1.64516	0.008
39DAP/reference	1.80323	0.007
41DAP/reference	1.68732	0.013
42DAP/reference	1.88434	0.006
43DAP/reference	2.16853	0.007
47DAP/reference	1.48091	0.224
52DAP/reference	1.6938	0.007
57DAP/reference	1.98277	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.33472	0.234
17DAP/reference	1.16966	0.176
27DAP/reference	1.40783	0.028
39DAP/reference	1.15607	0.366
41DAP/reference	1.07316	0.502
42DAP/reference	1.04372	1
43DAP/reference	0.93284	0.438
47DAP/reference	1.08753	0.556
52DAP/reference	1.26536	0.006
57DAP/reference	1.1607	0.214

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65466	0.033
17DAP/reference	1.31564	0.518
27DAP/reference	2.19845	0.028
39DAP/reference	1.98096	0.006
41DAP/reference	2.1777	0.01
42DAP/reference	1.79074	0.037
43DAP/reference	1.82904	0.022
47DAP/reference	1.05076	1
52DAP/reference	1.99482	0.112
57DAP/reference	1.24485	0.153

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97291	1
26DAP/20DAP	1.10774	0.953
34DAP/26DAP	1.0388	1
51DAP/34DAP	1.6384	0.087
52DAP/51DAP	0.84531	1
53DAP/52DAP	2.08648	0.047
55DAP/53DAP	0.88401	0.709
57DAP/55DAP	0.92696	0.694
62DAP/57DAP	1.08502	0.935
68DAP/62DAP	1.50978	0.142
68DAP/14DAP	1.40176	0.094

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.05548	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.46288	0.577
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
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	0.99649
12-2/M82	N/A	N/A
12-4/M82	0.93977
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	0.92692
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	1.02669	1
IL2-6/WTpooled	1.19325	0.584
IL7-5/WTpooled	1.57149
IL7-3/WTpooled	0.89528	1
IL12-4/WTpooled	0.79226	0.581
IL1-4/WTpooled	1.15705	0.426
WT/WTpooled	0.9502	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	0.94778	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03552	0.921
DC3000/delta hrp 6h	1.09669	1
DC3000/delta hrp 12h	0.74884	1
DC3000/delta hrp 24h	0.66291	0.049

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02183	1
DC3000 delta B/DC3000 delta AB	1.01386	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09004	1
Exp 36h	0.56873	0.393
Exp 60h	0.59695	0.249

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0698	1
Var 0h	0.84147	0.933
Var 12h I row2-row1	1.01546	1
Var 12h NI row2-row1	1.00855	1
Var 36h I row2-row1	1.121	0.309
Var 36h NI row2-row1	1.02596	1
Var 60h I row2-row1	0.5241	0.293
Var 60h NI row2-row1	1.04341	1
Time course 0hI-0hNI	0.9925	1
Time course 12hI-12hNI	1.02629	0.818
Time course 36hI-36hNI	1.03815	0.722
Time course 60hI-60hNI	1.33104	0.01

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)	1.04268	0.408
transgenic ySAMdc/azygous control (breaker)	0.64668	0.142
transgenic ySAMdc/azygous control (red)	0.87438	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96574	0.263

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.88338	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.50037	1
Manapal/WT (break)	2.73413	0.13
Manapal/WT (red)	1.97191	0.222