Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.16.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06631	0.893
27DAP/17DAP	1.18006	0.852
39DAP/27DAP	1.62599	0.121
41DAP/39DAP	0.79005	0.281
42DAP/41DAP	0.98775	1
43DAP/42DAP	0.90036	0.788
47DAP/43DAP	1.00499	0.851
52DAP/47DAP	1.00427	0.803
57DAP/52DAP	1.04741	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96066	0.371
17DAP/reference	0.92858	0.208
27DAP/reference	0.99202	0.741
39DAP/reference	0.96155	0.5
41DAP/reference	0.92532	0.201
42DAP/reference	0.93275	0.064
43DAP/reference	0.96949	0.5
47DAP/reference	0.9336	0.013
52DAP/reference	0.85277	0.031
57DAP/reference	0.89256	0.023

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01145	0.947
27DAP/17DAP	0.99046	0.919
39DAP/27DAP	1.02554	0.718
41DAP/39DAP	1.07699	0.817
42DAP/41DAP	0.96365	0.687
43DAP/42DAP	0.9615	0.503
47DAP/43DAP	1.00349	0.973
52DAP/47DAP	1.01712	0.933
57DAP/52DAP	1.03565	0.753
57DAP/7DAP	1.0965	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97559	0.55
17DAP/reference	0.97197	0.518
27DAP/reference	0.96969	0.43
39DAP/reference	0.90777	0.264
41DAP/reference	0.86958	0.107
42DAP/reference	0.99385	0.675
43DAP/reference	1.07328	0.83
47DAP/reference	0.93707	0.222
52DAP/reference	0.98464	0.571
57DAP/reference	0.85923	0.071

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99673	0.907
17DAP/reference	0.90449	0.143
27DAP/reference	0.98834	0.619
39DAP/reference	0.89616	0.047
41DAP/reference	0.8378	0.046
42DAP/reference	0.88658	0.025
43DAP/reference	0.9982	0.761
47DAP/reference	0.92253	0.123
52DAP/reference	0.93841	0.131
57DAP/reference	0.93226	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94831	0.362
17DAP/reference	1.01566	0.918
27DAP/reference	0.98401	0.624
39DAP/reference	0.96131	0.328
41DAP/reference	0.93561	0.264
42DAP/reference	0.92378	0.445
43DAP/reference	1.03306	1
47DAP/reference	0.9106	0.132
52DAP/reference	1.06965	0.674
57DAP/reference	0.7329	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.03763	0.966
26DAP/20DAP	0.92605	1
34DAP/26DAP	0.96645	0.97
51DAP/34DAP	0.94229	0.571
52DAP/51DAP	1.03124	0.776
53DAP/52DAP	0.9469	0.758
55DAP/53DAP	0.93155	0.515
57DAP/55DAP	1.108	0.805
62DAP/57DAP	1.02519	1
68DAP/62DAP	1.0547	0.864
68DAP/14DAP	1.11972	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01055	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.54176
Mature Green Tomato/Ripe Tomato	0.75706	0.119
Immature Eggplant/Mature Eggplant	0.66464
Ripe Pepper/Ripe Tomato	1.70108
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99168	1
1-1-2/M82	1.07237	1
12-2/M82	0.93196	0.692
12-4/M82	1.00608	1
1-3/M82	0.8366	0.441
2-1-1/M82	1.04264	1
2-1/M82	1.18669	0.345
2-6/M82	0.97487	1
3-2/M82	1.04252
4-1-1/M82	0.92947	1
4-1/M82	1.08512	0.466
4-3-2/M82	1.13685	0.284
4-3/M82	1.02788	1
5-3/M82	0.91479	0.642
6-2/M82	1.04602	1
6-3/M82	1.01721	1
7-1/M82	1.01356	0.539
7-2/M82	1.06523	1
9-3-2/M82	1.15878	1

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	0.8042
IL12-4/WTpooled	1.02511	1
IL1-4/WTpooled	0.71373
WT/WTpooled	1.20413	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	1.04935

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01299	0.921
DC3000/delta hrp 6h	0.94105	0.95
DC3000/delta hrp 12h	1.01526	1
DC3000/delta hrp 24h	1.09892	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.07655	0.229
DC3000 delta B/DC3000 delta AB	1.07833	0.453

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00523	1
Exp 36h	0.82412	0.406
Exp 60h	0.79831	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95326	1
Var 0h	0.94296	1
Var 12h I row2-row1	1.13669	0.187
Var 12h NI row2-row1	0.95101	0.466
Var 36h I row2-row1	0.91788	1
Var 36h NI row2-row1	0.97781	0.852
Var 60h I row2-row1	1.16387	1
Var 60h NI row2-row1	1.00011	1
Time course 0hI-0hNI	1.08949	0.799
Time course 12hI-12hNI	1.05436	0.734
Time course 36hI-36hNI	0.99686	0.768
Time course 60hI-60hNI	1.24067	0.009

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)	0.96264	0.3
transgenic ySAMdc/azygous control (breaker)	0.97053	0.49
transgenic ySAMdc/azygous control (red)	0.95884	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01739	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.22372	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.38208	1
Manapal/WT (break)	1.05565	1
Manapal/WT (red)	0.85382	0.184