MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Gene	Rank	description	Value Type	Network Comparison Type	Interaction Map	red	Filtered	network_comparison	green

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Showing element 1 to 42 of 42 in total

Value Type  : Ranked
Interaction Map  : High confidence
red  : 88.2482
Filtered  : 1
green  : 110.265

Rank	description	Network Comparison Type	network_comparison
83	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Divided	1.24949
84	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]
85	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
86	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
87	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
88	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
89	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
90	necdin. [swissprot;acc:q99608]
91	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
92	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
93	melanoma antigen, family b, 6. [refseq;acc:nm_173523]
94	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
95	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
96	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
97	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
98	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
99	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
100	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
101	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
102	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
103	trophinin. [swissprot;acc:q12816]
301	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Subtracted	22.0168
302	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]
303	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
304	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
305	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
306	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
307	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
308	necdin. [swissprot;acc:q99608]
309	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
310	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
311	melanoma antigen, family b, 6. [refseq;acc:nm_173523]
312	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
313	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
314	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
315	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
316	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
317	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
318	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
319	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
320	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
321	trophinin. [swissprot;acc:q12816]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.