Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.13.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90541	0.683
27DAP/17DAP	1.29179	0.847
39DAP/27DAP	0.82562	0.319
41DAP/39DAP	1.02239	0.545
42DAP/41DAP	1.2025	0.841
43DAP/42DAP	0.88756	0.801
47DAP/43DAP	1.14312	0.873
52DAP/47DAP	1.54293	0.31
57DAP/52DAP	0.99501	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85163	0.109
17DAP/reference	1.13424	0.092
27DAP/reference	0.98348	0.711
39DAP/reference	0.92812	0.381
41DAP/reference	1.01201	1
42DAP/reference	0.79146	0.009
43DAP/reference	0.97862	0.708
47DAP/reference	0.87988	0.06
52DAP/reference	1.06013	0.695
57DAP/reference	1.02409	0.876

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08937	0.728
27DAP/17DAP	1.04284	0.923
39DAP/27DAP	1.13803	0.378
41DAP/39DAP	1.03172	1
42DAP/41DAP	1.08165	0.719
43DAP/42DAP	1.04602	0.664
47DAP/43DAP	1.16588	0.121
52DAP/47DAP	0.91428	0.316
57DAP/52DAP	0.89961	0.532
57DAP/7DAP	1.09181	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93619	0.27
17DAP/reference	0.98062	0.447
27DAP/reference	1.18042	0.131
39DAP/reference	1.15258	0.371
41DAP/reference	1.1454	0.177
42DAP/reference	1.08931	0.686
43DAP/reference	1.1404	0.408
47DAP/reference	0.92238	0.383
52DAP/reference	0.91364	0.196
57DAP/reference	1.14461	0.214

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01158	0.97
17DAP/reference	0.93461	0.389
27DAP/reference	0.91264	0.282
39DAP/reference	0.83898	0.129
41DAP/reference	0.7961	0.063
42DAP/reference	0.79272	0.039
43DAP/reference	1.12607	0.515
47DAP/reference	0.93064	0.087
52DAP/reference	0.92774	0.239
57DAP/reference	0.97863	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01839	1
17DAP/reference	1.06982	0.602
27DAP/reference	1.08393	0.552
39DAP/reference	1.1374	0.087
41DAP/reference	1.04659	0.939
42DAP/reference	1.01736	1
43DAP/reference	0.93096	0.305
47DAP/reference	0.99966	0.626
52DAP/reference	1.12002	0.526
57DAP/reference	0.92651	0.262

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.02315	1
26DAP/20DAP	1.1362	0.7
34DAP/26DAP	0.76281	0.619
51DAP/34DAP	0.73561	0.442
52DAP/51DAP	0.98394	1
53DAP/52DAP	1.34576	0.819
55DAP/53DAP	0.89287	0.515
57DAP/55DAP	1.04515	1
62DAP/57DAP	1.02728	1
68DAP/62DAP	1.0979	0.919
68DAP/14DAP	0.73165	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.06572	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	54.2681	1
Mature Green Tomato/Ripe Tomato	0.06045	0.017
Immature Eggplant/Mature Eggplant	0.45191
Ripe Pepper/Ripe Tomato	0.72485
Mature Eggplant/Ripe Tomato	0.4745	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04992	1
1-1-2/M82	1.0917	1
12-2/M82	0.98577	0.955
12-4/M82	0.95702
1-3/M82	0.90459	1
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.04107	0.594
3-2/M82	1.03189
4-1-1/M82	0.99992	1
4-1/M82	1.65308
4-3-2/M82	0.96551
4-3/M82	1.42013	1
5-3/M82	1.04435	1
6-2/M82	1.17794	1
6-3/M82	0.99279	1
7-1/M82	1.09077	1
7-2/M82	0.98212	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.37403	0.365
IL2-6/WTpooled	0.98314	1
IL7-5/WTpooled	1.28606	1
IL7-3/WTpooled	1.14541	1
IL12-4/WTpooled	1.0269	1
IL1-4/WTpooled	1.46109	0.426
WT/WTpooled	0.95783	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	1.11747	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04328	0.921
DC3000/delta hrp 6h	1.22962	0.777
DC3000/delta hrp 12h	0.9787	1
DC3000/delta hrp 24h	1.38332	0.044

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	1.47761

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.22535	1
Exp 36h	1.67782	0.693
Exp 60h	1.06258	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06517	1
Var 0h	1.02263	1
Var 12h I row2-row1	1.09706	0.443
Var 12h NI row2-row1	1.2409	1
Var 36h I row2-row1	1.29236	0.41
Var 36h NI row2-row1	1.16724	1
Var 60h I row2-row1	0.70049	0.374
Var 60h NI row2-row1	0.81794	0.516
Time course 0hI-0hNI	1.20175	0.537
Time course 12hI-12hNI	0.91893	0.522
Time course 36hI-36hNI	1.38747	0.035
Time course 60hI-60hNI	8.43889	0.008

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)	1.33598	0.235
transgenic ySAMdc/azygous control (breaker)	1.52695	1
transgenic ySAMdc/azygous control (red)	1.82831	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9478	0.085

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.23545	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.19104	1
Manapal/WT (break)	0.85404	0.333
Manapal/WT (red)	0.95092	0.607