Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.12.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.20868	0.336
27DAP/17DAP	1.00141	1
39DAP/27DAP	1.02398	1
41DAP/39DAP	0.83505	0.213
42DAP/41DAP	1.15048	0.882
43DAP/42DAP	1.07727	1
47DAP/43DAP	0.9544	0.828
52DAP/47DAP	1.14852	0.847
57DAP/52DAP	1.09509	0.987

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06064	0.252
17DAP/reference	1.06246	0.161
27DAP/reference	1.06285	0.227
39DAP/reference	1.10347	0.027
41DAP/reference	1.03342	0.759
42DAP/reference	1.03882	0.144
43DAP/reference	0.98424	0.728
47DAP/reference	1.06325	0.101
52DAP/reference	1.06581	0.335
57DAP/reference	0.94651	0.176

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04933	0.63
27DAP/17DAP	N/A	N/A
39DAP/27DAP	0.92834	0.514
41DAP/39DAP	1.00223	1
42DAP/41DAP	0.99785	0.91
43DAP/42DAP	0.95061	0.351
47DAP/43DAP	1.06851	0.61
52DAP/47DAP	N/A	N/A
57DAP/52DAP	0.97021	0.657
57DAP/7DAP	0.88957	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86892	0.078
17DAP/reference	0.931	0.124
27DAP/reference	0.86386	0.012
39DAP/reference	0.92103	0.023
41DAP/reference	0.94531	0.166
42DAP/reference	0.903	0.03
43DAP/reference	0.88642	0.011
47DAP/reference	0.9158	0.128
52DAP/reference	0.9005	0.017
57DAP/reference	0.93491	0.042

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06131	0.308
17DAP/reference	1.16593	0.013
27DAP/reference	0.99257	0.642
39DAP/reference	1.08066	0.207
41DAP/reference	0.98196	0.441
42DAP/reference	1.02231	0.951
43DAP/reference	0.99601	0.801
47DAP/reference	1.03733	0.572
52DAP/reference	1.06213	0.034
57DAP/reference	1.17357	0.066

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90723	0.092
17DAP/reference	1.00451	1
27DAP/reference	0.94267	0.119
39DAP/reference	0.92777	0.021
41DAP/reference	0.92359	0.019
42DAP/reference	0.92271	0.019
43DAP/reference	0.95982	0.468
47DAP/reference	0.97068	0.396
52DAP/reference	0.97781	0.732
57DAP/reference	0.85563	0.02

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00434	1
26DAP/20DAP	1.20552	0.334
34DAP/26DAP	1.03543	1
51DAP/34DAP	0.95854	0.674
52DAP/51DAP	0.69466
53DAP/52DAP	0.99105	0.938
55DAP/53DAP	0.88208	0.163
57DAP/55DAP	1.13592	0.407
62DAP/57DAP	1.3007	0.868
68DAP/62DAP	0.71838	0.429
68DAP/14DAP	0.81509	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.13232	0.212

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93453	0.551
Mature Green Tomato/Ripe Tomato	1.3061	0.149
Immature Eggplant/Mature Eggplant	0.75914	0.134
Ripe Pepper/Ripe Tomato	1.06346	1
Mature Eggplant/Ripe Tomato	1.50613	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97217
1-1-2/M82	0.85595	1
12-2/M82	N/A	N/A
12-4/M82	0.96931	1
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	1.25421
3-2/M82	1.03938	0.84
4-1-1/M82	0.93311
4-1/M82	0.93162
4-3-2/M82	1.03048	1
4-3/M82	0.91664
5-3/M82	0.95301	1
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.78421
7-2/M82	1.06688
9-3-2/M82	1.05192	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.76696	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.3139	1
IL12-4/WTpooled	1.09735	0.785
IL1-4/WTpooled	0.65703
WT/WTpooled	1.11976	0.789

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	1.16624	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93154	1
DC3000/delta hrp 6h	1.05222	1
DC3000/delta hrp 12h	1.03383	1
DC3000/delta hrp 24h	1.05473	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.12125	0.16
DC3000 delta B/DC3000 delta AB	1.06794	0.462

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.46271	1
Exp 36h	1.22825	1
Exp 60h	1.48845	0.215

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97528	1
Var 0h	1.15319	0.594
Var 12h I row2-row1	0.99458	1
Var 12h NI row2-row1	1.07988	1
Var 36h I row2-row1	1.14539	0.41
Var 36h NI row2-row1	0.86892	0.549
Var 60h I row2-row1	1.02596	1
Var 60h NI row2-row1	0.9019	0.298
Time course 0hI-0hNI	0.9447	0.452
Time course 12hI-12hNI	1.05648	0.49
Time course 36hI-36hNI	1.25861	0.401
Time course 60hI-60hNI	1.6346	0.009

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)	0.87968	0.299
transgenic ySAMdc/azygous control (breaker)	0.76662	0.15
transgenic ySAMdc/azygous control (red)	0.84821	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99695	0.712

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.11607	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.76194	0.172
Manapal/WT (break)	0.86587	1
Manapal/WT (red)	0.89031	0.274