Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.13.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.52603	0.244
27DAP/17DAP	0.9851	0.941
39DAP/27DAP	1.52211	0.8
41DAP/39DAP	1.18458	0.814
42DAP/41DAP	0.96349	1
43DAP/42DAP	0.97952	0.91
47DAP/43DAP	1.76354	0.216
52DAP/47DAP	1.56451	0.156
57DAP/52DAP	0.9128	0.85

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97774	0.562
17DAP/reference	0.99619	0.858
27DAP/reference	0.97357	0.623
39DAP/reference	1.00712	0.885
41DAP/reference	0.98064	0.667
42DAP/reference	0.92203	0.088
43DAP/reference	0.91409	0.316
47DAP/reference	1.10105	0.032
52DAP/reference	1.10727	0.548
57DAP/reference	1.00148	0.845

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91791	0.388
27DAP/17DAP	0.75882	0.135
39DAP/27DAP	1.1177	0.483
41DAP/39DAP	0.92137	0.53
42DAP/41DAP	0.97332	0.746
43DAP/42DAP	0.98685	0.902
47DAP/43DAP	1.0256	0.948
52DAP/47DAP	0.99785	0.947
57DAP/52DAP	1.33353	0.116
57DAP/7DAP	1.39794

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81749	0.138
17DAP/reference	0.98748	0.518
27DAP/reference	1.00663	0.8
39DAP/reference	0.94581	0.354
41DAP/reference	0.89756	0.116
42DAP/reference	1.02917	1
43DAP/reference	0.88628	0.139
47DAP/reference	0.7173	0.057
52DAP/reference	0.96736	0.435
57DAP/reference	0.82992	0.03

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94599	0.592
17DAP/reference	0.94211	0.337
27DAP/reference	0.96785	0.423
39DAP/reference	1.02996	0.956
41DAP/reference	0.7762	0.013
42DAP/reference	1.0281	0.934
43DAP/reference	1.18036	0.532
47DAP/reference	1.01111	0.77
52DAP/reference	1.10261	0.596
57DAP/reference	0.97966	0.649

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75502	0.043
17DAP/reference	1.05658	0.712
27DAP/reference	1.19342	0.034
39DAP/reference	0.97972	0.544
41DAP/reference	0.96167	0.512
42DAP/reference	0.96232	0.445
43DAP/reference	0.81594	0.03
47DAP/reference	1.08152	0.443
52DAP/reference	0.89264	0.342
57DAP/reference	1.13796	0.385

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01601	0.966
26DAP/20DAP	2.3399
34DAP/26DAP	1.47036	1
51DAP/34DAP	0.63875
52DAP/51DAP	0.62473	1
53DAP/52DAP	1.04617	0.901
55DAP/53DAP	1.08394	0.589
57DAP/55DAP	0.96599	0.867
62DAP/57DAP	1.09399	0.569
68DAP/62DAP	0.94523	0.787
68DAP/14DAP	1.06613	0.958

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.9948	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.08727	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.08961	0.224
Mature Eggplant/Ripe Tomato	0.08004	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25365	0.877
1-1-2/M82	1.06711	1
12-2/M82	0.96687
12-4/M82	1.107	1
1-3/M82	0.7701	0.351
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.00519	1
3-2/M82	1.13676
4-1-1/M82	0.96108	1
4-1/M82	1.58281
4-3-2/M82	N/A	N/A
4-3/M82	1.06763	1
5-3/M82	0.93286	1
6-2/M82	N/A	N/A
6-3/M82	1.10783	1
7-1/M82	0.75919
7-2/M82	0.95751
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97221	1
IL2-6/WTpooled	0.88945	0.473
IL7-5/WTpooled	0.56706
IL7-3/WTpooled	1.13688	0.362
IL12-4/WTpooled	0.93276	1
IL1-4/WTpooled	0.85747	0.699
WT/WTpooled	0.99661	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	1.01605	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10348	0.875
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.00881	1
DC3000/delta hrp 24h	0.95959	0.75

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	1.41505

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	1.02279	1
Var 0h	1.01962	1
Var 12h I row2-row1	1.15871	0.242
Var 12h NI row2-row1	0.61135	0.367
Var 36h I row2-row1	0.99952	1
Var 36h NI row2-row1	0.59256	0.378
Var 60h I row2-row1	1.064	0.502
Var 60h NI row2-row1	1.03812	1
Time course 0hI-0hNI	1.04618	0.852
Time course 12hI-12hNI	1.54745	0.43
Time course 36hI-36hNI	1.1878	0.316
Time course 60hI-60hNI	2.0452	0.01

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)	1.7267	0.321
transgenic ySAMdc/azygous control (breaker)	1.26381	0.248
transgenic ySAMdc/azygous control (red)	0.99412	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98157	0.323

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.42361	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00246	1
Manapal/WT (break)	0.815	0.299
Manapal/WT (red)	1.11794	1