Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.12.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42354	0.428
27DAP/17DAP	0.8307	0.597
39DAP/27DAP	5.09607	0.025
41DAP/39DAP	0.92487	0.582
42DAP/41DAP	1.83086	0.696
43DAP/42DAP	2.4936	0.077
47DAP/43DAP	1.01033	1
52DAP/47DAP	0.44105	0.035
57DAP/52DAP	0.66935	0.591

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.54113	0.034
17DAP/reference	0.25647	0.007
27DAP/reference	0.26708	0.005
39DAP/reference	0.67204	0.064
41DAP/reference	0.37811	0.009
42DAP/reference	2.28427	0.001
43DAP/reference	10.0511	0.006
47DAP/reference	9.1012	0.001
52DAP/reference	1.68237	0.205
57DAP/reference	2.42918	0.229

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70607	0.046
27DAP/17DAP	1.17594	0.639
39DAP/27DAP	1.84742	0.044
41DAP/39DAP	1.86262	0.656
42DAP/41DAP	1.13274	1
43DAP/42DAP	1.25083	0.192
47DAP/43DAP	1.33752	0.121
52DAP/47DAP	0.94492	0.884
57DAP/52DAP	1.09476	0.753
57DAP/7DAP	1.30614	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.70978	0.059
17DAP/reference	0.71771	0.011
27DAP/reference	0.73208	0.01
39DAP/reference	0.72515	0.012
41DAP/reference	0.62648	0.015
42DAP/reference	0.73912	0.011
43DAP/reference	0.67597	0.012
47DAP/reference	1.12784	0.915
52DAP/reference	0.63887	0.013
57DAP/reference	0.6891	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.48704	0.008
17DAP/reference	0.23571	0.003
27DAP/reference	0.61524	0.032
39DAP/reference	0.40304	0.008
41DAP/reference	0.34422	0.005
42DAP/reference	0.63223	0.03
43DAP/reference	0.99407	0.569
47DAP/reference	0.94659	0.349
52DAP/reference	0.24856	0.003
57DAP/reference	0.51285	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71558	0.061
17DAP/reference	0.68513	0.154
27DAP/reference	0.70195	0.048
39DAP/reference	0.6262	0.007
41DAP/reference	0.73486	0.018
42DAP/reference	1.34182	0.576
43DAP/reference	3.58446	0.052
47DAP/reference	8.65104	0.004
52DAP/reference	1.76603	0.674
57DAP/reference	0.55153	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15269	1
26DAP/20DAP	1.22807	0.518
34DAP/26DAP	1.57079	1
51DAP/34DAP	1.2935	0.988
52DAP/51DAP	1.99917	0.038
53DAP/52DAP	0.74806	0.107
55DAP/53DAP	1.45004	0.039
57DAP/55DAP	0.57196	0.031
62DAP/57DAP	0.44751	0.05
68DAP/62DAP	1.63175	0.813
68DAP/14DAP	1.45274	0.033

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.37705	0.025

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.35148	0.028
Immature Eggplant/Mature Eggplant	21.4313	0.05
Ripe Pepper/Ripe Tomato	0.13812	0.224
Mature Eggplant/Ripe Tomato	0.08283	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	2.00069	0.505
1-1-2/M82	2.71375	1
12-2/M82	0.98387	0.955
12-4/M82	3.79627	1
1-3/M82	2.72274	0.255
2-1-1/M82	1.22953	0.422
2-1/M82	0.64213	0.345
2-6/M82	1.66802	0.351
3-2/M82	1.35628	0.717
4-1-1/M82	2.01681	0.977
4-1/M82	9.37767	0.853
4-3-2/M82	2.09016	0.253
4-3/M82	1.68729	1
5-3/M82	0.80726	1
6-2/M82	2.77151	0.253
6-3/M82	1.34547	1
7-1/M82	1.03954	1
7-2/M82	1.69298	0.299
9-3-2/M82	3.1809	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.33121	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95988	1
DC3000/delta hrp 6h	1.01802	1
DC3000/delta hrp 12h	0.94332	1
DC3000/delta hrp 24h	1.15315	0.254

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.49645	0.042
DC3000 delta B/DC3000 delta AB	1.84519	0.079

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.45079	0.254
Exp 36h	2.02103	0.349
Exp 60h	2.02158	0.22

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99955	1
Var 0h	0.48868	0.237
Var 12h I row2-row1	1.02352	0.736
Var 12h NI row2-row1	1.09204	0.649
Var 36h I row2-row1	1.2465	0.908
Var 36h NI row2-row1	0.87408	0.645
Var 60h I row2-row1	0.95846	0.952
Var 60h NI row2-row1	0.82901	0.932
Time course 0hI-0hNI	0.98455	0.967
Time course 12hI-12hNI	1.37265	0.012
Time course 36hI-36hNI	2.62009	0.005
Time course 60hI-60hNI	2.35104	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)	0.66603	0.229
transgenic ySAMdc/azygous control (breaker)	0.76469	0.173
transgenic ySAMdc/azygous control (red)	0.98027	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00154	0.958

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69209	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.88456	1
Manapal/WT (break)	1.09946	1
Manapal/WT (red)	0.74629	0.242