Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.3.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01158	0.919
27DAP/17DAP	1.10164	0.871
39DAP/27DAP	1.4796	0.426
41DAP/39DAP	1.22995	0.413
42DAP/41DAP	1.33292	0.712
43DAP/42DAP	0.88825	0.665
47DAP/43DAP	1.03055	0.92
52DAP/47DAP	0.92218	0.702
57DAP/52DAP	1.05891	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65617	0.008
17DAP/reference	1.55959	0.1
27DAP/reference	1.32487	0.03
39DAP/reference	1.26721	0.524
41DAP/reference	1.6132	0.312
42DAP/reference	1.60781	0.021
43DAP/reference	1.32895
47DAP/reference	1.18226	1
52DAP/reference	1.33852	0.088
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86083	0.299
27DAP/17DAP	1.03021	0.98
39DAP/27DAP	1.04486	0.845
41DAP/39DAP	1.0469	0.837
42DAP/41DAP	1.01304	1
43DAP/42DAP	0.96936	0.618
47DAP/43DAP	0.89809	0.559
52DAP/47DAP	1.36303	0.221
57DAP/52DAP	1.17332	0.571
57DAP/7DAP	0.53271

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.66819	0.024
17DAP/reference	2.3756	0.006
27DAP/reference	2.14516	0.007
39DAP/reference	1.98201	0.005
41DAP/reference	2.58162	0.008
42DAP/reference	2.08373	0.007
43DAP/reference	2.41213	0.008
47DAP/reference	2.72148	0.015
52DAP/reference	1.86963	0.011
57DAP/reference	1.83483	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.55448	0.104
17DAP/reference	1.71978	0.012
27DAP/reference	1.20337	0.292
39DAP/reference	1.24194	0.194
41DAP/reference	1.5177	0.025
42DAP/reference	1.38251	0.011
43DAP/reference	1.42439	0.647
47DAP/reference	1.38632	0.009
52DAP/reference	1.2705	0.008
57DAP/reference	1.45488	0.016

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.99783	0.016
17DAP/reference	1.43665	0.264
27DAP/reference	3.14784	0.013
39DAP/reference	2.66791	0.005
41DAP/reference	2.34964	0.011
42DAP/reference	1.94917	0.023
43DAP/reference	2.31409	0.016
47DAP/reference	1.35223	0.035
52DAP/reference	2.4533	0.028
57DAP/reference	2.92715	0.012

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.75969	0.915
26DAP/20DAP	1.16042	1
34DAP/26DAP	1.79337	1
51DAP/34DAP	0.94721	0.863
52DAP/51DAP	2.42038	0.083
53DAP/52DAP	0.94081	0.772
55DAP/53DAP	1.21726	0.366
57DAP/55DAP	0.68171	0.057
62DAP/57DAP	1.21151	0.002
68DAP/62DAP	0.78274	0.464
68DAP/14DAP	0.77501	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66613	0.031

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.09435	0.898
Immature Eggplant/Mature Eggplant	3.95916	0.05
Ripe Pepper/Ripe Tomato	0.08882	0.224
Mature Eggplant/Ripe Tomato	0.43407	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.09031	0.877
1-1-2/M82	0.99217	1
12-2/M82	1.16318	1
12-4/M82	0.99735	1
1-3/M82	0.92963	0.501
2-1-1/M82	1.04376	1
2-1/M82	0.73085
2-6/M82	1.07298	1
3-2/M82	1.0161
4-1-1/M82	0.85582	1
4-1/M82	1.21315	0.466
4-3-2/M82	1.12632
4-3/M82	1.17237	1
5-3/M82	1.09571	1
6-2/M82	1.04022	1
6-3/M82	1.03544	1
7-1/M82	0.94899
7-2/M82	0.83232	0.578
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01268	1
IL2-6/WTpooled	1.20052	0.419
IL7-5/WTpooled	0.79894	1
IL7-3/WTpooled	0.92777	1
IL12-4/WTpooled	1.0138	1
IL1-4/WTpooled	1.0589	1
WT/WTpooled	0.87051	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	1.38505	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02621	0.921
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.12237	1
DC3000/delta hrp 24h	1.10809	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.08875	0.333
DC3000 delta B/DC3000 delta AB	1.20264	0.433

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.12709	1
Exp 36h	N/A	N/A
Exp 60h	1.33185	0.399

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	N/A	N/A
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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	0.98852	1
transgenic ySAMdc/azygous control (red)	0.9903	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93468	0.568

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.88094	0.307
Manapal/WT (break)	0.95007	1
Manapal/WT (red)	0.78576	0.181