Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.11.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04134	1
27DAP/17DAP	1.17319	0.845
39DAP/27DAP	0.79746	0.462
41DAP/39DAP	2.09312	0.423
42DAP/41DAP	1.14438	1
43DAP/42DAP	1.03604	0.945
47DAP/43DAP	0.96615	0.799
52DAP/47DAP	1.41639	0.425
57DAP/52DAP	1.09099	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00543	0.824
17DAP/reference	1.05415	0.039
27DAP/reference	1.05255	0.33
39DAP/reference	0.99105	0.874
41DAP/reference	1.01769	0.91
42DAP/reference	0.86349	0.006
43DAP/reference	0.98451	0.763
47DAP/reference	0.88536	0.002
52DAP/reference	0.84377	0.102
57DAP/reference	0.89161	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9677	0.697
27DAP/17DAP	1.08861	0.694
39DAP/27DAP	1.08592	0.541
41DAP/39DAP	0.97867	0.98
42DAP/41DAP	1.04143	0.852
43DAP/42DAP	1.09175	0.324
47DAP/43DAP	1.02095	0.951
52DAP/47DAP	0.9666	0.913
57DAP/52DAP	1.00084	0.926
57DAP/7DAP	1.32041	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8007	0.088
17DAP/reference	0.75658	0.017
27DAP/reference	0.79299	0.01
39DAP/reference	0.8656	0.013
41DAP/reference	0.80511	0.013
42DAP/reference	0.80225	0.01
43DAP/reference	0.80093	0.013
47DAP/reference	0.84063	0.057
52DAP/reference	0.82945	0.012
57DAP/reference	0.88166	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99966	0.93
17DAP/reference	0.99196	0.711
27DAP/reference	0.8609	0.104
39DAP/reference	0.85078	0.072
41DAP/reference	0.82525	0.059
42DAP/reference	0.77079	0.039
43DAP/reference	1.02057	0.874
47DAP/reference	0.98161	0.459
52DAP/reference	0.93405	0.131
57DAP/reference	1.10985	0.166

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77909	0.044
17DAP/reference	0.93889	0.452
27DAP/reference	0.81589	0.043
39DAP/reference	0.83066	0.033
41DAP/reference	0.8257	0.032
42DAP/reference	0.67706	0.015
43DAP/reference	0.74229	0.04
47DAP/reference	0.9123	0.348
52DAP/reference	0.78914	0.142
57DAP/reference	0.59566	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95154	1
26DAP/20DAP	0.93576	1
34DAP/26DAP	1.03254	1
51DAP/34DAP	0.93359	0.436
52DAP/51DAP	0.97488	1
53DAP/52DAP	1.0344	0.83
55DAP/53DAP	1.10588	0.452
57DAP/55DAP	1.03314	1
62DAP/57DAP	1.20036	0.257
68DAP/62DAP	0.93175	0.722
68DAP/14DAP	0.65611	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81556	0.115

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.66967	0.132
Immature Eggplant/Mature Eggplant	0.71326	0.063
Ripe Pepper/Ripe Tomato	1.17004	1
Mature Eggplant/Ripe Tomato	1.25075	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98611	0.961
1-1-2/M82	0.86583	1
12-2/M82	1.33133	1
12-4/M82	1.04482
1-3/M82	0.93577	1
2-1-1/M82	1.07605	0.764
2-1/M82	1.09676
2-6/M82	1.06914	0.695
3-2/M82	0.88182	1
4-1-1/M82	1.02749	1
4-1/M82	0.97325	0.737
4-3-2/M82	0.92156	1
4-3/M82	0.74843	0.72
5-3/M82	0.98676	1
6-2/M82	0.99447	1
6-3/M82	0.75242	1
7-1/M82	0.85853	0.803
7-2/M82	1.09562	0.385
9-3-2/M82	1.00803	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.86555	0.243
IL2-6/WTpooled	0.80294	0.473
IL7-5/WTpooled	0.98767
IL7-3/WTpooled	1.17912	1
IL12-4/WTpooled	1.01657	1
IL1-4/WTpooled	0.89199	0.834
WT/WTpooled	0.94711	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	1.11628	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95989	1
DC3000/delta hrp 6h	0.88719	0.95
DC3000/delta hrp 12h	0.59957
DC3000/delta hrp 24h	0.98442	0.957

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.97266	1
DC3000 delta B/DC3000 delta AB	0.98917	1

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	1.02495	1
Var 0h	0.50178	1
Var 12h I row2-row1	1.10323	0.324
Var 12h NI row2-row1	0.92564	0.627
Var 36h I row2-row1	0.77278	0.805
Var 36h NI row2-row1	1.10896	1
Var 60h I row2-row1	1.23606	0.562
Var 60h NI row2-row1	1.32879	0.904
Time course 0hI-0hNI	1.10977	0.764
Time course 12hI-12hNI	1.02121	0.85
Time course 36hI-36hNI	0.96008	0.25
Time course 60hI-60hNI	1.32246	0.011

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)	0.91578	0.295
transgenic ySAMdc/azygous control (breaker)	0.93967	0.49
transgenic ySAMdc/azygous control (red)	1.00555	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.005	0.811

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.7802	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.84423	1
Manapal/WT (break)	1.10678	0.381
Manapal/WT (red)	1.00272	1