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

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Showing element 2158 to 2207 of 3228 in total

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

description	Rank	network_comparison	red	green
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074]	2387	1.00392	211.301	210.475
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072]	2450	1.00316	213.85	213.177
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436]	2686	1.00091	219.829	219.629
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062]	2530	1.00224	212.464	211.99
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065]	2545	1.00191	213.494	213.088
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	352	1.09728	242.14	265.696
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171]	2142	1.00688	206.443	207.864
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0]	1505	1.0181	216.158	212.316
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	188	1.14179	226.582	198.444
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	343	1.0973	241.625	265.136
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	189	1.14179	226.582	198.444
protein bap28. [swissprot;acc:q9h583]	1013	1.03239	244.312	236.647
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6]	1819	1.01164	220.462	217.926
protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8]	3131	1	0.00001	0.00001
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312]	1587	1.0163	220.129	216.598
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42]	3206	1	0.00001	0.00001
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	1570	1.01646	221.128	224.767
protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822]	2874	1	0.00001	0.00001
protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79]	3219
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]	1357	1.02208	228.409	223.475
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	13	1.3585	288.754	212.554
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	3102	1	0.00001	0.00001
protein cgi-147. [swissprot;acc:q9y3e5]	1490	1.01903	221.961	226.186
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]	539	1.06708	236.964	252.86
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	2188	1.00662	209.54	208.162
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	45	1.27066	204.641	161.051
protein hspc134 (protein cda04). [swissprot;acc:q9by43]	130	1.21277	94	114
protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]	3020	1	0.00001	0.00001
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]	2501	1.00272	217.398	216.809
protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655]	2857	1	0.00001	0.00001
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]	2399	1.00374	182.4	183.083
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723]	2398	1.00375	182.395	183.079
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	967	1.03426	211.987	204.964
protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759]	3186	1	0.00001	0.00001
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]	975	1.03426	211.987	204.964
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	1604	1.01593	214.984	211.614
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	1607	1.01588	214.982	211.622
protein kinase nyd-sp25. [refseq;acc:nm_033516]	1868	1.01085	207.642	209.895
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817]	2308	1.00505	215.543	214.459
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	55	1.26134	320.927	254.434
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	2014	1.00912	217.676	215.709
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]	2013	1.00913	217.662	215.693
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	2294	1.00527	162.331	163.187
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	37	1.27273	322	253
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	41
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	39
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	592	1.06298	91.63	97.4011
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	489	1.07257	231.276	215.627

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.