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

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Showing element 268 to 317 of 3228 in total

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

description	Rank	network_comparison	green	red
aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	1420	1.02084	208.229	203.979
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	2064	1.00833	205.939	207.655
aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728]	2544	1.00192	212.262	212.67
ammecr1 protein. [refseq;acc:nm_015365]	1577	1.01645	218.982	222.585
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	52	1.26667	105	133
amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	139	1.20415	225.68	271.752
amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]	2490	1.00284	195.08	194.527
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380]	3191	1	0.00001	0.00001
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	2636	1.00128	195.384	195.635
anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]	2663	1.00107	204.549	204.768
anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366]	2679	1.00096	189.959	190.142
androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	240	1.11785	254.15	227.357
angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]	2586	1.00154	213.75	213.422
angiomotin. [refseq;acc:nm_133265]	2585
anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	143	1.20408	49	59
ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]	2519	1.00234	216.341	215.835
ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]	2518
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]	805	1.04425	221.785	212.386
annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995]	1088	1.0295	213.378	219.673
annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]	1094	1.02938	213.385	219.655
antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]	2418	1.00359	218.984	218.2
apg3p; pc3-96 protein. [refseq;acc:nm_022488]	169	1.18722	98.0548	82.5916
apical-like protein (apxl protein). [swissprot;acc:q13796]	362	1.09641	211.136	231.492
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	248	1.11719	212.41	237.302
apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	1606	1.0159	204.662	207.916
apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114]	2151	1.00686	219.366	217.871
apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574]	1293	1.024	228.46	233.942
apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	1014	1.03238	235.422	243.045
apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]	1132	1.02731	212.675	218.484
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	1111	1.02766	212.123	217.99
apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797]	2421	1.00359	209.454	210.205
apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481]	2531	1.00221	215.787	216.264
aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	2690	1.00077	188.046	188.191
aquaporin 5. [swissprot;acc:p55064]	2692		188.048	188.192
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	2691			188.193
aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	2694	1.00075	188.081	188.223
arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7]	1184	1.02586	222.334	216.729
arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161]	1110	1.02769	222.782	216.78
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	947	1.03567	205.191	212.51
arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089]	1885	1.01064	206.615	204.44
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540]	1886	1.01061	206.682	204.512
arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]	1379	1.02148	213.875	218.47
arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815]	1478	1.01922	211.066	215.122
argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424]	2108	1.00726	217.93	216.36
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966]	1546	1.01701	221.474	217.769
arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	2235	1.0062	199.711	200.95
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	2798	1	0.00001	0.00001
armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	1714	1.01327	203.844	206.549
arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	2602	1.00141	225.192	224.875
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]	2632	1.00135	225.195	224.891

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.