Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.17.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89501	0.475
27DAP/17DAP	1.13368	1
39DAP/27DAP	3.34191	0.033
41DAP/39DAP	1.38834	0.483
42DAP/41DAP	2.49437	0.08
43DAP/42DAP	2.38882	0.703
47DAP/43DAP	0.88792	0.609
52DAP/47DAP	0.48182	0.057
57DAP/52DAP	0.93314	0.926

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94009	0.503
17DAP/reference	1.42779	0.057
27DAP/reference	1.0416	0.721
39DAP/reference	0.86402	0.083
41DAP/reference	1.09205	0.421
42DAP/reference	1.30228	0.004
43DAP/reference	0.93782	0.394
47DAP/reference	1.17694	0.154
52DAP/reference	1.26232	0.256
57DAP/reference	1.03776	0.952

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84362	0.323
27DAP/17DAP	0.86372	0.58
39DAP/27DAP	3.05182	0.016
41DAP/39DAP	0.73506	0.024
42DAP/41DAP	1.31775	0.026
43DAP/42DAP	1.44355	0.014
47DAP/43DAP	0.91031	0.339
52DAP/47DAP	0.96088	0.763
57DAP/52DAP	0.93297	0.463
57DAP/7DAP	1.23356	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14722	0.252
17DAP/reference	0.75783	0.02
27DAP/reference	0.78123	0.018
39DAP/reference	0.51034	0.011
41DAP/reference	0.59987	0.018
42DAP/reference	0.74621	0.01
43DAP/reference	0.76458	0.04
47DAP/reference	0.69962	0.036
52DAP/reference	0.64309	0.012
57DAP/reference	0.56689	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.32966	0.187
17DAP/reference	1.07321	0.839
27DAP/reference	0.99177	0.598
39DAP/reference	1.0882	0.956
41DAP/reference	1.06392	0.536
42DAP/reference	1.20893	0.118
43DAP/reference	1.06369	0.885
47DAP/reference	1.19147	0.164
52DAP/reference	1.26247	0.106
57DAP/reference	1.11179	0.705

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26263	0.025
17DAP/reference	0.91835	0.508
27DAP/reference	0.57225	0.031
39DAP/reference	0.91772	0.179
41DAP/reference	0.85833	0.132
42DAP/reference	0.90768	0.22
43DAP/reference	0.95814	0.432
47DAP/reference	1.09607	0.847
52DAP/reference	0.83865	0.247
57DAP/reference	1.14398	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16705	0.966
26DAP/20DAP	0.80204	0.512
34DAP/26DAP	1.31052	0.819
51DAP/34DAP	1.35755	0.207
52DAP/51DAP	1.02933	0.915
53DAP/52DAP	1.00613	1
55DAP/53DAP	0.90555	0.325
57DAP/55DAP	1.26692	0.301
62DAP/57DAP	0.88887	0.681
68DAP/62DAP	1.26378	1
68DAP/14DAP	2.28581

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	19.6296	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.32325	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	2.21552
Mature Eggplant/Ripe Tomato	0.2901	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.26111	0.742
1-1-2/M82	1.27369	1
12-2/M82	1.31007	1
12-4/M82	0.99282	1
1-3/M82	2.48
2-1-1/M82	1.44595	0.764
2-1/M82	1.16991	1
2-6/M82	1.90473	0.329
3-2/M82	1.07007	1
4-1-1/M82	1.36046	0.977
4-1/M82	0.74455
4-3-2/M82	2.37136	0.508
4-3/M82	1.08594	1
5-3/M82	0.96723	1
6-2/M82	N/A	N/A
6-3/M82	0.38138	0.796
7-1/M82	N/A	N/A
7-2/M82	1.59969	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89513	0.321
IL2-6/WTpooled	1.06352	0.659
IL7-5/WTpooled	1.19379	0.792
IL7-3/WTpooled	0.84466	0.283
IL12-4/WTpooled	1.03204	0.891
IL1-4/WTpooled	0.98959	1
WT/WTpooled	1.14505	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	1.50041	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.11264	0.894
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.18279	1
DC3000/delta hrp 24h	3.47143	0.022

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.33294	0.183
DC3000 delta B/DC3000 delta AB	1.01372	0.983

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	0.964	1
Var 0h	1.02816	1
Var 12h I row2-row1	1.45377	0.228
Var 12h NI row2-row1	1.0292	1
Var 36h I row2-row1	1.16746	0.742
Var 36h NI row2-row1	1.14143	1
Var 60h I row2-row1	0.9775	0.952
Var 60h NI row2-row1	0.94737	0.977
Time course 0hI-0hNI	1.06311	0.852
Time course 12hI-12hNI	1.57516	0.005
Time course 36hI-36hNI	2.2718	0.004
Time course 60hI-60hNI	5.78907	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.72952	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.4985	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.20924	1
Manapal/WT (red)	0.93766	0.728