Example of input CRE for state analysis |
Code |
Implication |
---|---|
M |
A or C |
R |
A or G |
W |
A or T |
S |
C or G |
Y |
C or T |
K |
G or T |
V |
A or C or G |
H |
A or C or T |
D |
A or G or T |
B |
C or G or T |
N |
G or A or T or C |
Category |
Ontology |
Classes Incuded in AtREA |
GOBP | Gene
Ontology Biological Process |
list of GOBP classes |
GOMF | Gene Onltology Molecular Function | list of GOMF classes |
GOCC | Gene Onlolotgy Cellular Component | list of GOCC classes |
MIPS | MIPS FUNCAT classes | list of MIPS FUNCAT classes |
ARACYC | ARACYC pathways | list of ARACYC classes |
Select
Class Category:
|
GOBP class |
Category | Description | Expression slides |
induced | Genes which show
induction in different microarray experiemnts |
|
repressed | Genes which show induction in different microarray experiemnts |
Expression slide |
Fold Cutoff (only for expression classes) : |
Select
Class Category:
|
User
Geneset |
CRE State(RCCGAC#ACGTGKC) | Number of gene with CRE state in class(Gc) | Number of genes in class(Tc) | Number of genes with CRE state in reference set(Fr) | Number of genes in reference set(Tr) | Class Occurrence of CRE State (Co=Fc/Tc) | Reference set occurrence of CRE state(Ro=Fr/Tr) | Occurrence Ratio (=Co/Ro) | Hypergeometic P-value | Genes which contain CRE state |
0#1
|
47 |
294 |
2617 |
22229 |
0.15986
|
0.11773 | 1.36 | 0.0181219106940625 | At1g10760,At1g11210,At1g12730,At1g22750,At1g22770,At1g28330,At1g53910,At1g67660,At1g75200,At1g78600,At1g79440,At1g80480,At2g15960,At2g21130,At2g28910,At2g33845,At2g34810,At2g38240,At2g39930,At3g10020,At3g15640,At3g29320,At3g43690,At3g47160,At3g53800,At4g03510,At4g11600,At4g14270,At4g15660,At4g18240,At4g19390,At4g26680,At4g30660,At4g33980,At4g34950,At4g39100,At5g14560,At5g42900,At5g47250,At5g47260,At5g50460,At5g54960,At5g59320,At5g60100,At5g60110,At5g61380,At5g67480 |
The output of
AtREA CRE features module (Figure 1) contains the
following columns
Column 1:
The CRE state.(the states for which the P-value of enrichment in the
selected gene set is less than 0.05 the rows are highlighted in
blue.
Column 2: Number of
genes from class which show the particular CRE state.
Column 4: Number of genes from the reference set which show the particular CRE state.
Column 5:
Number of genes in the reference set .
Column 6: Class occurrence of CRE state i.e. number of genes from the selected class which show the CRE state divided by the total number of genes in the selected class.
Column 7: Reference state occurrence of CRE state i.e. number of genes from the reference set which show the CRE state divided by the total number of genes in the reference set.
Column 9 (Hypergeometric P-vlaue) : the cumulative hypergeometric p-value of observing eqaul or greater number of CRE state containing promoters in a random set containing same number of genes.
Column 10 : list of genes from class which contain the CRE state in their upstream sequence.
CRE State(RCCGAC#ACGTGKC) | Number of gene with CRE state in class(Gc) | Number of genes in class(Tc) | Number of genes with CRE state in reference set(Fr) | Number of genes in reference set(Tr) | Class Occurrence of CRE State (Co=Fc/Tc) | Reference set occurrence of CRE state(Ro=Fr/Tr) | Occurrence Ratio (=Co/Ro) | Hypergeometic P-value | Genes which contain CRE state |
0#1 | 47 | 294 | 2617 | 22229 | 0.15986 | 0.11773 | 1.36 | 0.0181219106940625 | At1g10760,At1g11210,At1g12730,At1g22750,At1g22770,At1g28330,At1g53910,At1g67660,At1g75200,At1g78600,At1g79440,At1g80480,At2g15960,At2g21130,At2g28910,At2g33845,At2g34810,At2g38240,At2g39930,At3g10020,At3g15640,At3g29320,At3g43690,At3g47160,At3g53800,At4g03510,At4g11600,At4g14270,At4g15660,At4g18240,At4g19390,At4g26680,At4g30660,At4g33980,At4g34950,At4g39100,At5g14560,At5g42900,At5g47250,At5g47260,At5g50460,At5g54960,At5g59320,At5g60100,At5g60110,At5g61380,At5g67480 |
1#0 | 69 | 294 | 4179 | 22229 | 0.23469 | 0.18800 | 1.25 | 0.0257057006005127 | At1g06460,At1g14000,At1g26665,At1g27630,At1g29395,At1g48330,At1g49720,At1g49730,At1g51090,At1g68070,At1g68080,At1g75190,At1g80500,At2g01520,At2g02990,At2g15860,At2g15880,At2g16660,At2g19450,At2g21660,At2g21690,At2g23040,At2g25930,At2g28900,At2g34930,At2g37140,At2g39030,At2g39340,At2g42530,At2g42540,At3g15630,At3g18080,At3g26580,At3g28290,At3g43680,At3g47836,At3g47840,At3g47850,At3g47860,At3g48370,At3g50970,At3g53990,At3g59350,At3g62550,At4g03530,At4g04340,At4g11310,At4g11610,At4g12280,At4g19120,At4g23600,At4g30650,At4g34960,At4g35770,At5g05630,At5g06690,At5g06700,At5g07010,At5g25210,At5g26340,At5g42910,At5g47240,At5g48250,At5g50450,At5g57630,At5g61400,At5g62360,At5g63810,At5g63820 |
1#1 | 29 | 294 | 1042 | 22229 | 0.09864 | 0.04688 | 2.10 | 0.000136907956885787 | At1g17690,At1g22370,At1g27640,At1g69830,At1g75210,At1g76590,At2g15970,At2g17840,At2g22450,At2g29630,At2g38465,At2g47890,At3g05880,At3g10410,At3g22740,At3g46640,At3g47890,At3g48360,At3g63160,At4g01130,At4g02370,At4g03560,At4g09020,At4g27440,At4g33700,At5g03240,At5g15960,At5g52310,At5g57110 |