Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.4.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9631	0.743
27DAP/17DAP	0.79285	0.467
39DAP/27DAP	0.67982	0.257
41DAP/39DAP	0.63905	0.058
42DAP/41DAP	0.97191	1
43DAP/42DAP	1.41309	0.47
47DAP/43DAP	0.96216	0.828
52DAP/47DAP	0.51993	0.149
57DAP/52DAP	0.6875	0.745

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59071	0.007
17DAP/reference	1.3425	0.021
27DAP/reference	1.53161	0.01
39DAP/reference	1.20944	0.066
41DAP/reference	0.96446	0.542
42DAP/reference	1.01958	1
43DAP/reference	0.95963	0.675
47DAP/reference	0.90691	0.148
52DAP/reference	0.81812	0.077
57DAP/reference	0.85509	0.091

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22577	0.135
27DAP/17DAP	0.9738	0.878
39DAP/27DAP	0.64763	0.063
41DAP/39DAP	0.98834	0.934
42DAP/41DAP	1.03679	1
43DAP/42DAP	0.76232	0.022
47DAP/43DAP	0.82523	0.017
52DAP/47DAP	0.83351	0.251
57DAP/52DAP	1.05951	0.798
57DAP/7DAP	0.2188	0.157

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.39536	0.024
17DAP/reference	1.41555	0.006
27DAP/reference	0.9416	0.215
39DAP/reference	1.07328	0.12
41DAP/reference	0.90638	0.166
42DAP/reference	1.12403	0.174
43DAP/reference	1.02318	1
47DAP/reference	0.97886	0.671
52DAP/reference	1.04407	0.636
57DAP/reference	1.23591	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27581	0.38
17DAP/reference	1.11885	0.789
27DAP/reference	1.02836	0.902
39DAP/reference	0.87647	0.079
41DAP/reference	1.03735	0.878
42DAP/reference	0.87654	0.098
43DAP/reference	0.66222	0.008
47DAP/reference	0.83124	0.069
52DAP/reference	1.05412	0.5
57DAP/reference	0.63073	0.004

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.74763	0.015
17DAP/reference	1.74147	0.111
27DAP/reference	1.60361	0.015
39DAP/reference	1.42957	0.015
41DAP/reference	1.08836	0.554
42DAP/reference	1.37143	0.18
43DAP/reference	1.19519	0.246
47DAP/reference	1.49644	0.007
52DAP/reference	1.63911	0.039
57DAP/reference	1.49537	0.013

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96585	1
26DAP/20DAP	1.7768	0.106
34DAP/26DAP	0.93572	0.771
51DAP/34DAP	0.67928	0.06
52DAP/51DAP	0.97365	1
53DAP/52DAP	0.62645	0.049
55DAP/53DAP	0.4983	0.02
57DAP/55DAP	0.93942	0.744
62DAP/57DAP	1.09769	0.8
68DAP/62DAP	1.11861	0.939
68DAP/14DAP	0.66973	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.30091	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.84781	0.058
Mature Green Tomato/Ripe Tomato	4.76174	0.018
Immature Eggplant/Mature Eggplant	0.45961	0.063
Ripe Pepper/Ripe Tomato	3.03149	0.256
Mature Eggplant/Ripe Tomato	3.81522	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.34475	0.486
1-1-2/M82	1.22808	1
12-2/M82	1.09449	1
12-4/M82	1.64228	1
1-3/M82	1.86708	0.479
2-1-1/M82	1.14415	1
2-1/M82	0.36412	0.306
2-6/M82	3.89839	0.329
3-2/M82	0.67741
4-1-1/M82	1.47594	1
4-1/M82	0.28974
4-3-2/M82	2.42473	0.253
4-3/M82	1.38121	1
5-3/M82	0.80536	1
6-2/M82	1.11866	1
6-3/M82	0.97376	1
7-1/M82	0.94766	1
7-2/M82	N/A	N/A
9-3-2/M82	2.67828	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.81705	1
IL12-4/WTpooled	0.94438	1
IL1-4/WTpooled	0.76319	0.834
WT/WTpooled	0.84401	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	0.98576	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99445	1
DC3000/delta hrp 6h	0.98847	0.95
DC3000/delta hrp 12h	1.04057	1
DC3000/delta hrp 24h	0.52642	0.041

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.57777	0.023
DC3000 delta B/DC3000 delta AB	0.55652	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.03657	1
Exp 36h	0.79801	0.661
Exp 60h	0.67692	0.278

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	0.83519
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	0.96775	0.614
transgenic ySAMdc/azygous control (breaker)	1.60341	0.248
transgenic ySAMdc/azygous control (red)	2.30766	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.86165	0.083

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.77192	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	3.86857	0.083
Manapal/WT (break)	2.84809	0.183
Manapal/WT (red)	2.63703	0.142