Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39057	0.281
27DAP/17DAP	0.99877	1
39DAP/27DAP	2.20645	0.029
41DAP/39DAP	0.97944	0.724
42DAP/41DAP	0.997	1
43DAP/42DAP	1.12188	1
47DAP/43DAP	0.88782	0.628
52DAP/47DAP	1.26708	0.683
57DAP/52DAP	1.57918	0.706

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0618	0.611
17DAP/reference	0.89711	0.138
27DAP/reference	0.92313	0.275
39DAP/reference	0.8742	0.062
41DAP/reference	0.89395	0.154
42DAP/reference	0.95194	0.176
43DAP/reference	0.92593	0.36
47DAP/reference	0.98209	0.418
52DAP/reference	0.87936	0.102
57DAP/reference	1.03714	0.22

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.39155	0.164
27DAP/17DAP	1.23739	0.632
39DAP/27DAP	0.70909	0.311
41DAP/39DAP	0.79828	0.446
42DAP/41DAP	1.12693	0.886
43DAP/42DAP	1.36513	0.212
47DAP/43DAP	0.97518	0.923
52DAP/47DAP	0.97185	0.925
57DAP/52DAP	1.0619	0.864
57DAP/7DAP	1.2096

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81271	0.082
17DAP/reference	0.61672	0.016
27DAP/reference	0.57782	0.01
39DAP/reference	0.50075	0.011
41DAP/reference	0.48972	0.012
42DAP/reference	0.49953	0.01
43DAP/reference	0.45436	0.011
47DAP/reference	0.74817	0.128
52DAP/reference	0.56755	0.012
57DAP/reference	0.45035	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8763	0.342
17DAP/reference	1.00832	1
27DAP/reference	0.97104	0.452
39DAP/reference	0.90092	0.221
41DAP/reference	0.90414	0.087
42DAP/reference	0.94157	0.261
43DAP/reference	0.69076	0.029
47DAP/reference	0.8464	0.018
52DAP/reference	0.83064	0.018
57DAP/reference	0.80797	0.024

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32189	0.079
17DAP/reference	1.51099	0.17
27DAP/reference	1.00741	0.727
39DAP/reference	0.88568	0.122
41DAP/reference	0.77396	0.07
42DAP/reference	0.7383	0.059
43DAP/reference	0.95926	0.468
47DAP/reference	0.91216	0.224
52DAP/reference	0.78565	0.148
57DAP/reference	1.09915	0.814

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82437	0.585
26DAP/20DAP	1.1088	0.7
34DAP/26DAP	1.01886	1
51DAP/34DAP	1.84522	0.032
52DAP/51DAP	0.90589	1
53DAP/52DAP	1.61534	0.025
55DAP/53DAP	0.85774	0.489
57DAP/55DAP	1.02766	0.93
62DAP/57DAP	0.94687	0.871
68DAP/62DAP	1.16191	0.689
68DAP/14DAP	1.07488	0.85

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.72947	0.081

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.4608	0.058
Mature Green Tomato/Ripe Tomato	1.1403	0.948
Immature Eggplant/Mature Eggplant	0.6232	0.063
Ripe Pepper/Ripe Tomato	2.10299	0.258
Mature Eggplant/Ripe Tomato	3.91977	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.70536
12-2/M82	N/A	N/A
12-4/M82	1.13103
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	0.91234
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.85099	1
IL2-6/WTpooled	0.97991	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.9718	1
IL12-4/WTpooled	1.37734	0.673
IL1-4/WTpooled	1.44216
WT/WTpooled	1.04726	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	1.17733	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97352	1
DC3000/delta hrp 6h	1.17687
DC3000/delta hrp 12h	1.1099	1
DC3000/delta hrp 24h	0.82548	0.231

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.67554	0.024
DC3000 delta B/DC3000 delta AB	0.64263	0.021

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	1.0559	1
Var 0h	0.51377	1
Var 12h I row2-row1	0.94274	0.627
Var 12h NI row2-row1	0.94986	0.82
Var 36h I row2-row1	0.82658	1
Var 36h NI row2-row1	1.00841	1
Var 60h I row2-row1	0.81688	0.374
Var 60h NI row2-row1	1.01811	1
Time course 0hI-0hNI	1.06038	0.719
Time course 12hI-12hNI	1.01671	0.82
Time course 36hI-36hNI	0.93705	0.246
Time course 60hI-60hNI	0.49515	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)	0.89421	0.291
transgenic ySAMdc/azygous control (breaker)	1.40778	0.172
transgenic ySAMdc/azygous control (red)	1.14425	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84515	0.074

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.28267	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.40519	0.083
Manapal/WT (break)	3.22114	0.123
Manapal/WT (red)	2.67733	0.222