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

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Showing element 2180 to 2229 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

description	Rank	red	green	network_comparison
protein cgi-147. [swissprot;acc:q9y3e5]	2529	6436.43	6283	1.02442
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	2705	4137.61	4152.72	1.00365
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	2104	6916.14	7295.24	1.05481
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	86	4942.49	7037.32	1.42384
protein hspc134 (protein cda04). [swissprot;acc:q9by43]	150	11068	8508.5	1.30082
protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]	3020	0.00001	0.00001	1
protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]	3142
protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6]	2845
protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4]	1850	6158.6	6551.94	1.06387
protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655]	2857	0.00001	0.00001	1
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]	960	11773	10733.2	1.09688
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723]	965	11773.7	10733.8
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	664	6374.65	7145.59	1.12094
protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759]	3186	0.00001	0.00001	1
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]	672	6374.65	7145.59	1.12094
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	1022	6435.94	7045.75	1.09475
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	1023	6435.02	7044.65	1.09474
protein kinase nyd-sp25. [refseq;acc:nm_033516]	2637	6527.56	6608.61	1.01242
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817]	1711	5917.22	6322.72	1.06853
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	24	950.561	2108.52	2.21818
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	1568	5845.22	6267.34	1.07222
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]	1566	5846.67	6269.41	1.0723
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	490	15274.9	13346.9	1.14445
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	18	677.5	1865.5	2.75351
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	22
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	20
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	238	27642.5	22440.4	1.23182
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	527	4775.11	5438.18	1.13886
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	313	21644.2	18098.7	1.1959
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	1887	5438.6	5783.11	1.06335
protein sck (fragment). [swissprot;acc:p98077]	1827	5633.44	5997	1.06454
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	2576	5608.22	5712.39	1.01857
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	2023	3560.24	3364.84	1.05807
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	1988	3559.49	3360.39	1.05925
protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]	3135	0.00001	0.00001	1
protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437]	3127
protein transport protein sec24a (sec24-related protein a) (fragment). [swissprot;acc:o95486]	3056
protein transport protein sec24b (sec24-related protein b). [swissprot;acc:o95487]	2956
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	2910
protein transport protein sec24d (sec24-related protein d). [swissprot;acc:o94855]	2903
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	2079	3614.91	3423.89	1.05579
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	2078
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	2265	3612.45	3453.39	1.04606
protein x 0001. [refseq;acc:nm_016302]	1582	6376.12	6833.59	1.07175
protein x 0004. [refseq;acc:nm_016301]	16	2671	871	3.06659
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]	538	10603.5	12069.4	1.13825
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	1247	6278.76	6807.51	1.08421
protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124]	2789	0.00001	0.00001	1
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706]	1248	6275.86	6803.95	1.08415
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	248	6417.18	7859.6	1.22477

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.