Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.2.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04675	0.961
27DAP/17DAP	0.60801	0.068
39DAP/27DAP	0.8954	0.62
41DAP/39DAP	0.87997	0.602
42DAP/41DAP	1.29385	0.82
43DAP/42DAP	1.02818	1
47DAP/43DAP	1.30926	0.842
52DAP/47DAP	1.09232	0.886
57DAP/52DAP	1.45636	0.694

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16107	0.179
17DAP/reference	0.86537	0.169
27DAP/reference	0.71961	0.08
39DAP/reference	0.78423	0.049
41DAP/reference	0.65055	0.009
42DAP/reference	0.80926	0.028
43DAP/reference	0.94287	0.611
47DAP/reference	0.73274	0.006
52DAP/reference	0.66134	0.017
57DAP/reference	0.88149	0.086

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31442	0.271
27DAP/17DAP	0.97362	0.887
39DAP/27DAP	0.88318	0.507
41DAP/39DAP	1.4491	0.623
42DAP/41DAP	1.01032	0.887
43DAP/42DAP	1.05974	0.83
47DAP/43DAP	0.99199	0.928
52DAP/47DAP	1.01205	0.907
57DAP/52DAP	0.93936	0.685
57DAP/7DAP	2.23242	0.204

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.70939	0.028
17DAP/reference	1.53948	0.013
27DAP/reference	1.0257	0.974
39DAP/reference	1.20312	0.21
41DAP/reference	0.9717	0.512
42DAP/reference	1.17164	0.308
43DAP/reference	1.0386	1
47DAP/reference	0.73178	0.128
52DAP/reference	0.97926	0.523
57DAP/reference	0.99701	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05239	0.842
17DAP/reference	0.74716	0.089
27DAP/reference	0.79452	0.033
39DAP/reference	0.70456	0.014
41DAP/reference	0.82486	0.045
42DAP/reference	1.01469	0.594
43DAP/reference	0.88355	0.269
47DAP/reference	0.86045	0.053
52DAP/reference	0.64697	0.003
57DAP/reference	0.5774	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.81957	0.051
17DAP/reference	1.54871	0.206
27DAP/reference	0.94211	0.416
39DAP/reference	1.10756	0.792
41DAP/reference	1.01589	0.826
42DAP/reference	0.96557	0.552
43DAP/reference	0.86015	0.256
47DAP/reference	0.83947	0.199
52DAP/reference	0.98411	0.732
57DAP/reference	0.96561	0.483

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.20257	0.966
26DAP/20DAP	0.921	1
34DAP/26DAP	1.10573	1
51DAP/34DAP	0.94945	0.758
52DAP/51DAP	1.11721	0.888
53DAP/52DAP	0.86206	0.323
55DAP/53DAP	1.15909	0.733
57DAP/55DAP	1.01374	1
62DAP/57DAP	1.35449	0.622
68DAP/62DAP	1.75153	0.747
68DAP/14DAP	1.0737	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.44998

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.15221	0.06
Mature Green Tomato/Ripe Tomato	1.74346	0.022
Immature Eggplant/Mature Eggplant	0.63279	0.062
Ripe Pepper/Ripe Tomato	12.0631	0.256
Mature Eggplant/Ripe Tomato	4.54285	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.64082
1-1-2/M82	1.20245	1
12-2/M82	N/A	N/A
12-4/M82	1.17964	1
1-3/M82	1.22839
2-1-1/M82	1.72403	0.354
2-1/M82	0.78555
2-6/M82	N/A	N/A
3-2/M82	1.09211
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	1.62955	0.268
5-3/M82	0.90737	0.447
6-2/M82	N/A	N/A
6-3/M82	0.52161	0.375
7-1/M82	N/A	N/A
7-2/M82	0.99548
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.03456	1
IL2-6/WTpooled	1.22814	0.427
IL7-5/WTpooled	1.27552	0.587
IL7-3/WTpooled	1.72779	1
IL12-4/WTpooled	0.95207	1
IL1-4/WTpooled	1.73414	0.395
WT/WTpooled	1.06152	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	0.84843	0.197

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98158	1
DC3000/delta hrp 6h	0.95944	0.95
DC3000/delta hrp 12h	1.04772	1
DC3000/delta hrp 24h	0.92579	0.473

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.44595	0.023
DC3000 delta B/DC3000 delta AB	0.43026	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88806	1
Exp 36h	0.62348	0.434
Exp 60h	0.6389	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03821	1
Var 0h	0.88866	1
Var 12h I row2-row1	0.85863	0.705
Var 12h NI row2-row1	0.9865	1
Var 36h I row2-row1	0.84619	0.575
Var 36h NI row2-row1	1.30247	1
Var 60h I row2-row1	1.33549	0.562
Var 60h NI row2-row1	0.98017	1
Time course 0hI-0hNI	1.14166	0.867
Time course 12hI-12hNI	0.99323	0.984
Time course 36hI-36hNI	0.70426	0.023
Time course 60hI-60hNI	0.12111	0.005

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)	1.06144	0.798
transgenic ySAMdc/azygous control (breaker)	1.48938	0.248
transgenic ySAMdc/azygous control (red)	0.93397	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.7339	0.07

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.23023	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.65133	0.083
Manapal/WT (break)	6.55013	0.123
Manapal/WT (red)	2.15802	0.413