Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.2.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11069	0.77
27DAP/17DAP	1.38903	0.798
39DAP/27DAP	1.07209	1
41DAP/39DAP	1.2273	0.516
42DAP/41DAP	1.02769	1
43DAP/42DAP	1.12535	0.985
47DAP/43DAP	0.96793	0.851
52DAP/47DAP	0.84474	0.595
57DAP/52DAP	1.08174	0.935

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01437	0.814
17DAP/reference	1.01673	0.546
27DAP/reference	0.97487	0.428
39DAP/reference	0.99872	0.991
41DAP/reference	0.98096	0.542
42DAP/reference	0.95789	0.157
43DAP/reference	0.97689	0.691
47DAP/reference	0.95611	0.161
52DAP/reference	0.9234	0.283
57DAP/reference	1.10574	0.229

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01288	0.961
27DAP/17DAP	0.95821	0.684
39DAP/27DAP	0.94403	0.514
41DAP/39DAP	0.9657	0.849
42DAP/41DAP	1.04446	0.74
43DAP/42DAP	1.0397	0.297
47DAP/43DAP	1.00342	0.973
52DAP/47DAP	0.99739	0.97
57DAP/52DAP	0.90524	0.311
57DAP/7DAP	1.01231	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88916	0.168
17DAP/reference	0.90938	0.035
27DAP/reference	0.75118	0.012
39DAP/reference	0.86291	0.023
41DAP/reference	0.86901	0.062
42DAP/reference	0.80689	0.016
43DAP/reference	0.81529	0.015
47DAP/reference	0.89118	0.222
52DAP/reference	0.85685	0.035
57DAP/reference	0.93639	0.314

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04318	0.577
17DAP/reference	0.94188	0.214
27DAP/reference	0.98331	0.537
39DAP/reference	0.93358	0.095
41DAP/reference	0.9367	0.156
42DAP/reference	0.98659	0.482
43DAP/reference	1.0231	0.785
47DAP/reference	1.03102	0.621
52DAP/reference	1.02077	0.559
57DAP/reference	0.99821	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88798	0.059
17DAP/reference	1.13626	0.376
27DAP/reference	0.83429	0.062
39DAP/reference	0.83147	0.015
41DAP/reference	0.91601	0.04
42DAP/reference	0.85258	0.019
43DAP/reference	0.87588	0.021
47DAP/reference	0.9868	0.558
52DAP/reference	0.6954	0.128
57DAP/reference	1.02717	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00606	0.966
26DAP/20DAP	0.89543	0.512
34DAP/26DAP	0.92131	0.702
51DAP/34DAP	1.15858	0.387
52DAP/51DAP	0.96096	0.079
53DAP/52DAP	0.9506	0.772
55DAP/53DAP	1.01906	0.981
57DAP/55DAP	1.04518	0.906
62DAP/57DAP	0.91249	0.28
68DAP/62DAP	1.0657	0.821
68DAP/14DAP	1.17216	0.023

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.93928	0.322

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77715	0.23
Mature Green Tomato/Ripe Tomato	1.08921	0.69
Immature Eggplant/Mature Eggplant	0.96317	0.808
Ripe Pepper/Ripe Tomato	2.33485	0.258
Mature Eggplant/Ripe Tomato	1.12536	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03677	0.877
1-1-2/M82	0.99062	1
12-2/M82	0.98051	1
12-4/M82	0.9594	1
1-3/M82	0.97475	0.378
2-1-1/M82	0.93548	0.784
2-1/M82	1.01988	1
2-6/M82	0.96686	1
3-2/M82	0.70843
4-1-1/M82	1.02721	1
4-1/M82	0.93252	1
4-3-2/M82	1.01267	1
4-3/M82	0.98623	1
5-3/M82	0.99015	1
6-2/M82	1.0549	1
6-3/M82	1.03622	1
7-1/M82	1.10439
7-2/M82	0.90511	0.796
9-3-2/M82	0.89092	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.69674	0.358
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.50447	1
IL12-4/WTpooled	1.07711	0.891
IL1-4/WTpooled	1.20198
WT/WTpooled	1.01426	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	1.14581	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01288	0.921
DC3000/delta hrp 6h	0.97068	0.95
DC3000/delta hrp 12h	0.98873	1
DC3000/delta hrp 24h	1.02937	0.633

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.91669	0.273
DC3000 delta B/DC3000 delta AB	1.01824	0.703

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84529	1
Exp 36h	0.59979	0.41
Exp 60h	0.56083	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97469	1
Var 0h	0.99776	1
Var 12h I row2-row1	0.83039	0.39
Var 12h NI row2-row1	0.86395	0.546
Var 36h I row2-row1	0.9256	0.805
Var 36h NI row2-row1	0.98348	0.852
Var 60h I row2-row1	1.06952	0.271
Var 60h NI row2-row1	1.02961	1
Time course 0hI-0hNI	0.98147	0.935
Time course 12hI-12hNI	0.99855	1
Time course 36hI-36hNI	0.92368	0.129
Time course 60hI-60hNI	0.51532	0.006

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)	0.94494	0.377
transgenic ySAMdc/azygous control (breaker)	1.40552	0.248
transgenic ySAMdc/azygous control (red)	1.19271	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93939	0.058

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.47442	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.54733	0.083
Manapal/WT (break)	2.01439	0.123
Manapal/WT (red)	1.92437	0.126