Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.17.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08621	0.977
27DAP/17DAP	1.26968	0.839
39DAP/27DAP	1.37686	0.631
41DAP/39DAP	1.2521	0.451
42DAP/41DAP	1.0257	1
43DAP/42DAP	0.81624	0.705
47DAP/43DAP	0.76603	0.345
52DAP/47DAP	1.22443	0.971
57DAP/52DAP	0.9342	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30287	0.29
17DAP/reference	1.05292	0.492
27DAP/reference	1.12534	0.071
39DAP/reference	1.02011	1
41DAP/reference	1.15712	0.102
42DAP/reference	1.34811	0.027
43DAP/reference	1.24826	0.36
47DAP/reference	1.21303	0.105
52DAP/reference	1.61902	0.01
57DAP/reference	1.6578	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02482	1
27DAP/17DAP	0.99474	0.969
39DAP/27DAP	1.30485	0.102
41DAP/39DAP	0.95385	0.839
42DAP/41DAP	1.16917	0.559
43DAP/42DAP	0.93191	0.447
47DAP/43DAP	0.92323	0.373
52DAP/47DAP	0.78569	0.366
57DAP/52DAP	0.97294	0.732
57DAP/7DAP	0.8678	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86837	0.183
17DAP/reference	0.89214	0.192
27DAP/reference	0.78734	0.045
39DAP/reference	0.69797	0.02
41DAP/reference	0.80226	0.054
42DAP/reference	0.67194	0.016
43DAP/reference	0.94324	0.385
47DAP/reference	1.08869	0.791
52DAP/reference	0.80381	0.066
57DAP/reference	0.95037	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10607	0.695
17DAP/reference	1.14081	0.166
27DAP/reference	1.25841	0.041
39DAP/reference	1.2362	0.048
41DAP/reference	1.37249	0.046
42DAP/reference	1.26505	0.07
43DAP/reference	1.07606	0.633
47DAP/reference	1.08027	0.513
52DAP/reference	1.42182	0.038
57DAP/reference	1.01274	0.754

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74086	0.039
17DAP/reference	0.89759	0.205
27DAP/reference	0.91521	0.206
39DAP/reference	0.82362	0.04
41DAP/reference	0.857	0.132
42DAP/reference	1.20968	0.743
43DAP/reference	1.07165	0.738
47DAP/reference	1.40566	0.155
52DAP/reference	1.10508	0.724
57DAP/reference	1.44448	0.09

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90986	1
26DAP/20DAP	1.27384	0.238
34DAP/26DAP	1.00848	1
51DAP/34DAP	0.77599	0.098
52DAP/51DAP	0.8549	1
53DAP/52DAP	0.67386	0.159
55DAP/53DAP	0.84965	0.489
57DAP/55DAP	1.14597	0.898
62DAP/57DAP	1.1211	1
68DAP/62DAP	2.26568	0.737
68DAP/14DAP	1.85199	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.41901	0.105

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.19052	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.66763
Mature Eggplant/Ripe Tomato	0.56215	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.96034	1
12-2/M82	1.23453
12-4/M82	1.05419	0.611
1-3/M82	N/A	N/A
2-1-1/M82	1.00507
2-1/M82	N/A	N/A
2-6/M82	0.88177
3-2/M82	1.05557
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	1.06603	0.268
5-3/M82	1.03477	1
6-2/M82	N/A	N/A
6-3/M82	0.91852
7-1/M82	1.08427	0.87
7-2/M82	0.99289	1
9-3-2/M82	1.10802

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.7566	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00121	1
IL12-4/WTpooled	1.18385	0.673
IL1-4/WTpooled	0.94082	0.834
WT/WTpooled	1.04456	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	1.10774	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97579	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.05558	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.04365	0.408
DC3000 delta B/DC3000 delta AB	1.08363	0.457

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07807	1
Exp 36h	N/A	N/A
Exp 60h	1.04245	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98926	1
Var 0h	1.09943	1
Var 12h I row2-row1	0.9881	1
Var 12h NI row2-row1	1.11263	1
Var 36h I row2-row1	1.20751	0.41
Var 36h NI row2-row1	0.98013	0.852
Var 60h I row2-row1	0.83203	0.582
Var 60h NI row2-row1	0.9572	0.866
Time course 0hI-0hNI	1.06202	0.852
Time course 12hI-12hNI	0.95455	0.65
Time course 36hI-36hNI	1.0196	0.799
Time course 60hI-60hNI	1.11428	0.069

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)	0.91837	0.454
transgenic ySAMdc/azygous control (breaker)	0.96881	1
transgenic ySAMdc/azygous control (red)	0.71722	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	1.05517	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.94507	1
Manapal/WT (break)	0.91395	1
Manapal/WT (red)	1.08812	0.413