Attachment 'Supplementary_netbox-report.html'
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NetBox Report
Matching gene list (HUGO) from Plasma proteome candidates working in Radiobiology service and Pathways involved in human glioblastoma (TCGA, Nature 455, 1061-1068)
This report was auto-generated by NetBox on: Thu Jan 31 11:08:58 CET 2013
NetBox Parameters:
| Parameter |
Value |
|---|
| Gene File |
/media/8294-7434/MCP/fig/pathway/netbox/gbm_data/Altered_Plasma_Protein_List_From_Rabiology_Services.txt |
| Shortest Path Threshold |
2 |
| P-Value Linker Cut-Off |
5E-2 |
Network Discovered:
| Name |
Value |
|---|
| Number of input genes |
28 |
| Number of vertices in graph |
44 |
| Number of edges in graph |
71 |
| At shortest path threshold of: 2 and p-value cut-off of: 5E-2, I can connect 15 genes with 29 linker genes. |
Modules Detected:
| Module ID |
Number of Genes |
Genes |
| 0 |
14 |
RAP1A
CLIC4*
HSPA1A*
YWHAZ
RAF1*
PLD2*
BRAF*
ACTB
PRKCD*
MAPT*
CFL1*
CSNK1A1*
ACTC1*
SMARCA4*
|
| 1 |
12 |
ATF7IP*
HSPG2
ITGB1*
LGALS3BP
CFHR1
CRP
COMP
CFH*
NID1*
TTR*
FN1*
RBP4
|
| 2 |
9 |
KLKB1
CUBN*
TFRC
HGF*
HIF1A*
RANBP9*
ARNT*
TF
IGFBP3*
|
| 3 |
5 |
GFI1B*
CDK5R2*
NEBL*
ACTN1
PDLIM5*
|
| 4 |
4 |
C1orf103*
KLC2*
S100A8
GC
|
| * Linker gene was not present in the original input list, but is significantly connected to members of the input list. |
Linker Gene Details: Based on Global Network with: 9264 genes and 68111 edges.
| Gene Symbol |
Local Degree |
Global Degree |
Unadjusted P-Value |
FDR Adjusted P-Value |
Status |
| CLIC4 |
2 |
3 |
1,76496E-5 |
0,0006 |
Included in Network |
| NEBL |
2 |
4 |
3,52192E-5 |
0,0006 |
Included in Network |
| CDK5R2 |
2 |
6 |
8,76491E-5 |
0,0009 |
Included in Network |
| PDLIM5 |
2 |
7 |
0,0001 |
0,0010 |
Included in Network |
| KLC2 |
2 |
9 |
0,0002 |
0,0012 |
Included in Network |
| CFH |
2 |
10 |
0,0003 |
0,0012 |
Included in Network |
| CUBN |
2 |
10 |
0,0003 |
0,0012 |
Included in Network |
| TTR |
2 |
18 |
0,0009 |
0,0035 |
Included in Network |
| NID1 |
2 |
20 |
0,0011 |
0,0038 |
Included in Network |
| FN1 |
3 |
88 |
0,0012 |
0,0039 |
Included in Network |
| CFL1 |
2 |
23 |
0,0014 |
0,0041 |
Included in Network |
| BRAF |
2 |
24 |
0,0015 |
0,0041 |
Included in Network |
| IGFBP3 |
2 |
29 |
0,0023 |
0,0055 |
Included in Network |
| ACTC1 |
2 |
31 |
0,0026 |
0,0058 |
Included in Network |
| PLD2 |
2 |
32 |
0,0027 |
0,0058 |
Included in Network |
| RANBP9 |
2 |
37 |
0,0036 |
0,0072 |
Included in Network |
| SMARCA4 |
2 |
38 |
0,0038 |
0,0072 |
Included in Network |
| MAPT |
2 |
44 |
0,0051 |
0,0090 |
Included in Network |
| HGF |
2 |
48 |
0,0060 |
0,0101 |
Included in Network |
| CSNK1A1 |
2 |
50 |
0,0065 |
0,0104 |
Included in Network |
| HSPA1A |
2 |
60 |
0,0091 |
0,0137 |
Included in Network |
| ATF7IP |
2 |
61 |
0,0094 |
0,0137 |
Included in Network |
| GFI1B |
2 |
64 |
0,0103 |
0,0144 |
Included in Network |
| ARNT |
2 |
82 |
0,0163 |
0,0218 |
Included in Network |
| C1orf103 |
2 |
93 |
0,0205 |
0,0262 |
Included in Network |
| HIF1A |
2 |
99 |
0,0229 |
0,0282 |
Included in Network |
| ITGB1 |
2 |
104 |
0,0250 |
0,0297 |
Included in Network |
| RAF1 |
2 |
110 |
0,0276 |
0,0316 |
Included in Network |
| PRKCD |
2 |
117 |
0,0308 |
0,0340 |
Included in Network |
| JAK2 |
2 |
174 |
0,0598 |
0,0638 |
Pruned from Network |
| PRKACA |
2 |
233 |
0,0937 |
0,0967 |
Pruned from Network |
| TP53 |
2 |
262 |
0,1108 |
0,1108 |
Pruned from Network |
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