Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.15.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.24902	0.485
27DAP/17DAP	1.19612	0.804
39DAP/27DAP	0.77926	0.286
41DAP/39DAP	1.2595	0.233
42DAP/41DAP	1.04024	0.997
43DAP/42DAP	0.91517	0.806
47DAP/43DAP	1.09173	0.715
52DAP/47DAP	1.02857	0.973
57DAP/52DAP	0.96523	0.952

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20056	0.041
17DAP/reference	1.05537	0.412
27DAP/reference	1.16686	0.194
39DAP/reference	0.93265	0.624
41DAP/reference	1.30219	0.203
42DAP/reference	1.16521	0.103
43DAP/reference	1.0975	0.233
47DAP/reference	1.07828	0.365
52DAP/reference	1.34976	0.043
57DAP/reference	1.21091	0.122

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02645	0.762
27DAP/17DAP	1.02683	0.942
39DAP/27DAP	1.06448	0.596
41DAP/39DAP	1.01817	0.914
42DAP/41DAP	1.02808	0.947
43DAP/42DAP	1.04428	0.23
47DAP/43DAP	1.02265	0.901
52DAP/47DAP	0.9802	0.9
57DAP/52DAP	1.03383	0.832
57DAP/7DAP	1.13703	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99446	0.682
17DAP/reference	0.9449	0.338
27DAP/reference	0.82833	0.066
39DAP/reference	0.9235	0.264
41DAP/reference	0.96423	0.375
42DAP/reference	0.85653	0.189
43DAP/reference	0.92369	0.305
47DAP/reference	1.04694	1
52DAP/reference	0.91729	0.254
57DAP/reference	1.07575	0.536

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18413	0.083
17DAP/reference	1.19969	0.02
27DAP/reference	1.14883	0.239
39DAP/reference	1.49834	0.17
41DAP/reference	2.00863	0.006
42DAP/reference	1.52643	0.015
43DAP/reference	1.14548	0.785
47DAP/reference	1.2218	0.017
52DAP/reference	1.41091	0.006
57DAP/reference	1.28363	0.013

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93026	0.29
17DAP/reference	1.06269	0.712
27DAP/reference	0.84752	0.038
39DAP/reference	1.01329	1
41DAP/reference	0.95896	0.512
42DAP/reference	1.09903	1
43DAP/reference	1.07814	0.973
47DAP/reference	1.25154	0.093
52DAP/reference	0.93559	0.505
57DAP/reference	1.36014	0.347

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93926	1
26DAP/20DAP	0.95506	0.512
34DAP/26DAP	0.95552	0.826
51DAP/34DAP	0.95646	0.688
52DAP/51DAP	1.01054	0.925
53DAP/52DAP	1.02223	0.944
55DAP/53DAP	1.08273	0.834
57DAP/55DAP	0.99139	0.927
62DAP/57DAP	1.13824	0.935
68DAP/62DAP	0.73165	0.29
68DAP/14DAP	0.82036	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84185	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.9069	0.377
Immature Eggplant/Mature Eggplant	0.25535
Ripe Pepper/Ripe Tomato	0.13913
Mature Eggplant/Ripe Tomato	1.12452	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04867	0.877
1-1-2/M82	1.08629
12-2/M82	N/A	N/A
12-4/M82	0.81618	0.619
1-3/M82	0.78445
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.11291
3-2/M82	0.96392
4-1-1/M82	N/A	N/A
4-1/M82	0.84089	0.69
4-3-2/M82	0.85152	0.698
4-3/M82	0.71878
5-3/M82	0.98375	1
6-2/M82	0.80908
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.70781	0.434
9-3-2/M82	0.85553	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.69739	0.247
IL2-6/WTpooled	1.16099	0.395
IL7-5/WTpooled	0.87154	1
IL7-3/WTpooled	0.99826	1
IL12-4/WTpooled	0.87274	0.71
IL1-4/WTpooled	0.87224	0.699
WT/WTpooled	1.11908	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	1.47152	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96493	1
DC3000/delta hrp 6h	0.95923	0.95
DC3000/delta hrp 12h	1.11983	1
DC3000/delta hrp 24h	1.02514	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06241	0.441
DC3000 delta B/DC3000 delta AB	1.06918	0.415

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08479	1
Exp 36h	N/A	N/A
Exp 60h	0.87422	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99058	1
Var 0h	0.57952	0.222
Var 12h I row2-row1	1.08331	0.204
Var 12h NI row2-row1	0.87779	0.713
Var 36h I row2-row1	1.09554	1
Var 36h NI row2-row1	1.35826	1
Var 60h I row2-row1	1.14732	0.562
Var 60h NI row2-row1	1.28741	1
Time course 0hI-0hNI	1.0976	0.764
Time course 12hI-12hNI	1.07553	0.654
Time course 36hI-36hNI	1.02671	0.58
Time course 60hI-60hNI	1.29147	0.009

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)	1.15981	0.654
transgenic ySAMdc/azygous control (breaker)	0.75974	0.142
transgenic ySAMdc/azygous control (red)	1.05706	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93779	0.101

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.18722	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.00512	1
Manapal/WT (red)	1.06996	1