Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.7.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32628	0.162
27DAP/17DAP	1.09767	0.881
39DAP/27DAP	0.95496	0.7
41DAP/39DAP	0.86806	0.55
42DAP/41DAP	0.75438	0.397
43DAP/42DAP	0.88953	0.813
47DAP/43DAP	1.25121	0.405
52DAP/47DAP	1.15105	0.718
57DAP/52DAP	0.8954	0.869

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04805	1
17DAP/reference	0.97577	0.701
27DAP/reference	1.05243	0.771
39DAP/reference	0.8835	0.132
41DAP/reference	0.94498	0.542
42DAP/reference	0.96691	0.295
43DAP/reference	1.19449	0.152
47DAP/reference	1.10719	0.329
52DAP/reference	0.91031	0.215
57DAP/reference	1.04098	0.829

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.13081	0.581
27DAP/17DAP	1.22085	0.292
39DAP/27DAP	0.99174	0.943
41DAP/39DAP	1.18845	0.656
42DAP/41DAP	0.96557	0.721
43DAP/42DAP	0.88451	0.121
47DAP/43DAP	0.96155	0.833
52DAP/47DAP	0.9128	0.763
57DAP/52DAP	1.24634	0.341
57DAP/7DAP	11.2064

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88628	0.203
17DAP/reference	1.16468	0.297
27DAP/reference	1.1131	0.16
39DAP/reference	0.98872	0.64
41DAP/reference	0.96855	0.489
42DAP/reference	0.99446	0.675
43DAP/reference	1.12112	0.923
47DAP/reference	1.01204	1
52DAP/reference	1.03171	1
57DAP/reference	1.12083	0.198

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07065	0.634
17DAP/reference	0.91836	0.378
27DAP/reference	0.86884	0.22
39DAP/reference	0.85054	0.071
41DAP/reference	0.97471	0.481
42DAP/reference	0.79242	0.03
43DAP/reference	1.05008	0.919
47DAP/reference	0.91805	0.11
52DAP/reference	0.93792	0.351
57DAP/reference	1.10889	0.236

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82172	0.082
17DAP/reference	1.44295	0.511
27DAP/reference	1.10252	0.373
39DAP/reference	1.10394	0.365
41DAP/reference	1.0988	0.537
42DAP/reference	1.13126	0.658
43DAP/reference	1.11072	0.505
47DAP/reference	0.88144	0.063
52DAP/reference	0.86139	0.107
57DAP/reference	0.84568	0.083

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.19039	0.966
26DAP/20DAP	1.43569	0.162
34DAP/26DAP	0.92822	0.909
51DAP/34DAP	1.50257	0.759
52DAP/51DAP	0.93144	1
53DAP/52DAP	1.05075	0.858
55DAP/53DAP	0.9633	0.746
57DAP/55DAP	1.02992	0.927
62DAP/57DAP	0.98728	1
68DAP/62DAP	1.21427	0.767
68DAP/14DAP	0.93087	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10647	0.855

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.56642	0.053
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.93031
Mature Eggplant/Ripe Tomato	0.80756	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.46102
1-1-2/M82	1.04061
12-2/M82	0.71364
12-4/M82	1.10692
1-3/M82	N/A	N/A
2-1-1/M82	0.96484
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
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	1.5439	0.268
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.93707
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.44925	0.584
IL7-5/WTpooled	2.1329
IL7-3/WTpooled	0.99915	1
IL12-4/WTpooled	1.03126	0.646
IL1-4/WTpooled	1.06519	1
WT/WTpooled	0.9731	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	0.95748	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04553	0.921
DC3000/delta hrp 6h	1.38258	1
DC3000/delta hrp 12h	0.88871	1
DC3000/delta hrp 24h	1.08552	0.243

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	11.2169

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05448	1
Exp 36h	1.3839	1
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	0.97939	1
Var 0h	0.72372	1
Var 12h I row2-row1	1.23394	0.506
Var 12h NI row2-row1	0.99314	1
Var 36h I row2-row1	1.02258	1
Var 36h NI row2-row1	0.82582	0.262
Var 60h I row2-row1	1.03497	1
Var 60h NI row2-row1	0.85813	0.932
Time course 0hI-0hNI	0.86354	0.994
Time course 12hI-12hNI	1.03524	0.741
Time course 36hI-36hNI	0.95138	0.323
Time course 60hI-60hNI	1.10907	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)	0.79599	0.454
transgenic ySAMdc/azygous control (breaker)	0.95778	0.49
transgenic ySAMdc/azygous control (red)	1.03577	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99919	0.94

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.34191	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	1.2317	0.164