Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.12.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73775	0.464
27DAP/17DAP	0.93383	0.863
39DAP/27DAP	1.79535	0.047
41DAP/39DAP	0.54387	0.062
42DAP/41DAP	1.80584	0.519
43DAP/42DAP	1.00504	0.925
47DAP/43DAP	0.91746	0.693
52DAP/47DAP	0.99763	0.845
57DAP/52DAP	1.31004	0.883

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3845	0.012
17DAP/reference	1.03102	0.787
27DAP/reference	1.18545	0.084
39DAP/reference	1.07333	0.445
41DAP/reference	1.05368	0.714
42DAP/reference	1.36097	0.001
43DAP/reference	1.19139	0.008
47DAP/reference	0.92386	0.137
52DAP/reference	0.8012	0.049
57DAP/reference	0.98821	0.58

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.15392	0.414
27DAP/17DAP	1.03955	0.9
39DAP/27DAP	0.84322	0.068
41DAP/39DAP	1.09536	0.799
42DAP/41DAP	0.99114	0.85
43DAP/42DAP	0.91779	0.503
47DAP/43DAP	1.01284	0.957
52DAP/47DAP	0.8715	0.314
57DAP/52DAP	0.88342	0.169
57DAP/7DAP	0.76272	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.54013	0.124
17DAP/reference	1.53254	0.006
27DAP/reference	1.98271	0.006
39DAP/reference	1.55575	0.035
41DAP/reference	1.53183	0.008
42DAP/reference	1.44139	0.016
43DAP/reference	1.20359	0.06
47DAP/reference	1.3888	0.014
52DAP/reference	1.90206	0.011
57DAP/reference	1.63006	0.005

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16823	0.048
17DAP/reference	1.05386	0.723
27DAP/reference	1.08123	0.497
39DAP/reference	1.17786	0.035
41DAP/reference	0.97129	0.441
42DAP/reference	1.2162	0.099
43DAP/reference	0.93855	0.414
47DAP/reference	1.3597	0.01
52DAP/reference	0.85241	0.016
57DAP/reference	0.98674	0.68

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.38883	0.034
17DAP/reference	1.06762	0.689
27DAP/reference	1.30327	0.044
39DAP/reference	1.5299	0.013
41DAP/reference	1.53849	0.009
42DAP/reference	1.57024	0.009
43DAP/reference	1.194	0.894
47DAP/reference	0.98514	0.558
52DAP/reference	1.151	0.306
57DAP/reference	0.82999	0.028

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.55952	0.966
26DAP/20DAP	1.47429	0.288
34DAP/26DAP	1.10546	0.819
51DAP/34DAP	0.70498	0.088
52DAP/51DAP	0.79007	0.151
53DAP/52DAP	0.90445	0.374
55DAP/53DAP	0.67821	0.024
57DAP/55DAP	1.03167	0.94
62DAP/57DAP	1.30623	0.004
68DAP/62DAP	1.13276	0.759
68DAP/14DAP	1.52941	0.02

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.27276	0.034

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.48584	0.058
Mature Green Tomato/Ripe Tomato	1.86263	0.028
Immature Eggplant/Mature Eggplant	1.88259	0.05
Ripe Pepper/Ripe Tomato	0.76217	0.293
Mature Eggplant/Ripe Tomato	4.19489	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16666
1-1-2/M82	1.2968	1
12-2/M82	0.84739
12-4/M82	1.12397	1
1-3/M82	2.3507
2-1-1/M82	1.02481	1
2-1/M82	0.90461	0.322
2-6/M82	0.75722	0.33
3-2/M82	1.69694	0.84
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.49313	0.508
4-3/M82	1.68385	0.268
5-3/M82	0.89355	1
6-2/M82	2.21563	0.235
6-3/M82	N/A	N/A
7-1/M82	0.8853	1
7-2/M82	0.79638
9-3-2/M82	1.23265	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03932	1
IL2-6/WTpooled	1.03396	1
IL7-5/WTpooled	1.05775	1
IL7-3/WTpooled	1.03462	1
IL12-4/WTpooled	1.00109	1
IL1-4/WTpooled	1.00246	1
WT/WTpooled	0.97853	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	0.93629	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95366	1
DC3000/delta hrp 6h	1.13923	1
DC3000/delta hrp 12h	0.80502	1
DC3000/delta hrp 24h	3.90711	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95701
DC3000 delta B/DC3000 delta AB	0.86339	0.121

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03824	1
Exp 36h	1.46562	0.693
Exp 60h	1.5974	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97515	1
Var 0h	1.07074	1
Var 12h I row2-row1	0.8896	0.705
Var 12h NI row2-row1	1.15585	0.34
Var 36h I row2-row1	1.15144	0.298
Var 36h NI row2-row1	0.84076	0.361
Var 60h I row2-row1	0.82402	0.293
Var 60h NI row2-row1	0.99275	1
Time course 0hI-0hNI	0.91649	0.535
Time course 12hI-12hNI	0.97699	0.87
Time course 36hI-36hNI	1.07975	0.401
Time course 60hI-60hNI	1.2803	0.06

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)	0.95545	0.324
transgenic ySAMdc/azygous control (breaker)	1.11535	1
transgenic ySAMdc/azygous control (red)	1.05369	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.34955	0.11

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87011	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.55807	0.088
Manapal/WT (break)	0.93261	1
Manapal/WT (red)	1.3691	0.413