Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.5.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.19365	0.63
27DAP/17DAP	1.12555	0.872
39DAP/27DAP	0.79815	0.482
41DAP/39DAP	1.31669	0.331
42DAP/41DAP	1.12517	1
43DAP/42DAP	1.0616	0.937
47DAP/43DAP	0.85826	0.546
52DAP/47DAP	1.29623	0.635
57DAP/52DAP	0.95193	0.947

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58651	0.098
17DAP/reference	0.8367	0.104
27DAP/reference	0.84755	0.232
39DAP/reference	0.92153	0.342
41DAP/reference	0.88409	0.434
42DAP/reference	0.84271	0.001
43DAP/reference	0.94786	0.17
47DAP/reference	0.8043	0.001
52DAP/reference	0.7081	0.036
57DAP/reference	0.81722	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06161	0.642
27DAP/17DAP	0.8962	0.339
39DAP/27DAP	1.01307	0.799
41DAP/39DAP	0.97474	0.98
42DAP/41DAP	1.13955	0.415
43DAP/42DAP	0.89985	0.482
47DAP/43DAP	0.97756	0.909
52DAP/47DAP	1.06695	0.8
57DAP/52DAP	0.94381	0.428
57DAP/7DAP	0.93275	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.66675	0.091
17DAP/reference	0.77797	0.011
27DAP/reference	0.80515	0.01
39DAP/reference	0.8129	0.011
41DAP/reference	0.7605	0.039
42DAP/reference	0.83161	0.03
43DAP/reference	0.7071	0.011
47DAP/reference	0.42447	0.04
52DAP/reference	0.70292	0.019
57DAP/reference	0.69252	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.7331	0.009
17DAP/reference	0.65568	0.003
27DAP/reference	0.78566	0.022
39DAP/reference	0.6271	0.013
41DAP/reference	0.7483	0.028
42DAP/reference	0.83834	0.01
43DAP/reference	0.64828	0.021
47DAP/reference	0.83213	0.01
52DAP/reference	0.64635	0.004
57DAP/reference	0.66497	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76652	0.026
17DAP/reference	0.77086	0.214
27DAP/reference	0.82396	0.031
39DAP/reference	0.72835	0.009
41DAP/reference	0.71287	0.058
42DAP/reference	0.68039	0.059
43DAP/reference	0.70593	0.019
47DAP/reference	0.66797	0.01
52DAP/reference	0.64259	0.064
57DAP/reference	0.45688	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9782	1
26DAP/20DAP	0.81039	0.244
34DAP/26DAP	1.17713	1
51DAP/34DAP	1.01472	0.909
52DAP/51DAP	1.02188	0.939
53DAP/52DAP	1.05996	0.901
55DAP/53DAP	0.97476	0.852
57DAP/55DAP	1.05932	0.906
62DAP/57DAP	1.09953	0.021
68DAP/62DAP	0.95988	0.7
68DAP/14DAP	1.03631	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.82588	0.083

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.21078	0.363
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.02409

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.92977	0.944
1-1-2/M82	0.96893	1
12-2/M82	1.14626
12-4/M82	0.95885	1
1-3/M82	0.68406	0.378
2-1-1/M82	0.7366
2-1/M82	N/A	N/A
2-6/M82	1.35119	0.505
3-2/M82	0.82168
4-1-1/M82	1.10389
4-1/M82	1.0656
4-3-2/M82	0.85928	1
4-3/M82	1.31717
5-3/M82	0.97603	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.05107
7-2/M82	1.02486	1
9-3-2/M82	0.79167	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.04625	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.01871	1
IL12-4/WTpooled	0.89939	1
IL1-4/WTpooled	1.14935	1
WT/WTpooled	1.01533	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	0.94156	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96185	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.07434	1
DC3000/delta hrp 24h	1.12641	0.356

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.59422	0.024
DC3000 delta B/DC3000 delta AB	0.67242	0.025

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00014	1
Var 0h	1.23821	0.594
Var 12h I row2-row1	1.14431	0.736
Var 12h NI row2-row1	0.94112	0.494
Var 36h I row2-row1	0.89806	1
Var 36h NI row2-row1	1.16039	0.482
Var 60h I row2-row1	1.35062	0.562
Var 60h NI row2-row1	1.08847	0.904
Time course 0hI-0hNI	1.05189	0.603
Time course 12hI-12hNI	0.99563	1
Time course 36hI-36hNI	1.01976	1
Time course 60hI-60hNI	0.21161	0.005

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)	1.27772	0.571
transgenic ySAMdc/azygous control (breaker)	1.01249	1
transgenic ySAMdc/azygous control (red)	1.14164	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99899	0.911

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83256	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.58607	0.083
Manapal/WT (break)	1.0742	1
Manapal/WT (red)	1.05716	1