Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.12.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74667	0.159
27DAP/17DAP	1.04291	1
39DAP/27DAP	0.91652	0.62
41DAP/39DAP	0.76811	0.256
42DAP/41DAP	0.86601	0.774
43DAP/42DAP	0.97669	0.925
47DAP/43DAP	1.21187	0.769
52DAP/47DAP	1.02812	0.991
57DAP/52DAP	0.86319	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38255	0.013
17DAP/reference	1.24415	0.018
27DAP/reference	1.19516	0.021
39DAP/reference	1.16045	0.083
41DAP/reference	1.00178	1
42DAP/reference	1.04683	0.731
43DAP/reference	0.92166	0.107
47DAP/reference	1.03288	1
52DAP/reference	0.8895	0.105
57DAP/reference	0.87251	0.118

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.6982	0.056
27DAP/17DAP	1.08215	0.761
39DAP/27DAP	0.66103	0.04
41DAP/39DAP	0.86437	0.495
42DAP/41DAP	0.93649	0.617
43DAP/42DAP	1.10299	0.478
47DAP/43DAP	0.77133	0.026
52DAP/47DAP	1.04533	0.945
57DAP/52DAP	0.98969	0.845
57DAP/7DAP	0.75529	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85361	0.168
17DAP/reference	0.93888	0.167
27DAP/reference	0.95947	0.348
39DAP/reference	0.84355	0.039
41DAP/reference	0.8797	0.049
42DAP/reference	0.85475	0.086
43DAP/reference	0.82289	0.016
47DAP/reference	0.88769	0.222
52DAP/reference	0.78734	0.013
57DAP/reference	0.8205	0.016

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.52053	0.111
17DAP/reference	1.54102	0.011
27DAP/reference	1.33757	0.235
39DAP/reference	1.10667	0.3
41DAP/reference	0.97103	0.451
42DAP/reference	1.16177	0.118
43DAP/reference	1.60109	0.135
47DAP/reference	1.12947	0.128
52DAP/reference	1.15881	0.043
57DAP/reference	1.1894	0.188

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92232	0.268
17DAP/reference	1.23824	0.253
27DAP/reference	0.91667	0.097
39DAP/reference	1.10236	0.342
41DAP/reference	0.94523	0.371
42DAP/reference	1.08805	0.818
43DAP/reference	0.89179	0.305
47DAP/reference	1.05577	0.68
52DAP/reference	0.95823	0.623
57DAP/reference	1.31877	0.052

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8694	0.787
26DAP/20DAP	0.72883	0.512
34DAP/26DAP	1.30869	1
51DAP/34DAP	1.35646	0.281
52DAP/51DAP	1.19111	0.565
53DAP/52DAP	0.78247	0.498
55DAP/53DAP	1.25316	0.876
57DAP/55DAP	1.05193	0.921
62DAP/57DAP	1.02865	1
68DAP/62DAP	0.94178	0.769
68DAP/14DAP	0.57695	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97341	0.358

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	5.55779	0.058
Mature Green Tomato/Ripe Tomato	3.01447	0.022
Immature Eggplant/Mature Eggplant	0.47797	0.063
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	10.4188	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11779	0.409
1-1-2/M82	1.3017
12-2/M82	1.46113
12-4/M82	0.94967	1
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	0.80746	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.63865
4-1/M82	1.78098
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.95998	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.98828
9-3-2/M82	1.19322

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.8731	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	2.16729	1
IL12-4/WTpooled	1.32241
IL1-4/WTpooled	3.72661	1
WT/WTpooled	1.01328	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	0.56372	0.256

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95959	1
DC3000/delta hrp 6h	1.02696	1
DC3000/delta hrp 12h	1.13325	1
DC3000/delta hrp 24h	0.59188	0.036

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.33294	0.025
DC3000 delta B/DC3000 delta AB	0.40947	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.10771	1
Exp 36h	0.67523	0.589
Exp 60h	0.57132	0.32

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03266	1
Var 0h	0.95782	1
Var 12h I row2-row1	0.84919	0.338
Var 12h NI row2-row1	0.95281	0.713
Var 36h I row2-row1	0.89196	0.805
Var 36h NI row2-row1	1.29789	1
Var 60h I row2-row1	1.04166	1
Var 60h NI row2-row1	1.15015	0.904
Time course 0hI-0hNI	1.00724	1
Time course 12hI-12hNI	0.83584	0.1
Time course 36hI-36hNI	0.6838	0.023
Time course 60hI-60hNI	0.18698	0.006

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)	0.84402	0.409
transgenic ySAMdc/azygous control (breaker)	1.27986	1
transgenic ySAMdc/azygous control (red)	1.10362	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94509	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	5.7782	0.228

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.45006	0.087
Manapal/WT (break)	1.09226	1
Manapal/WT (red)	3.58119	0.142