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

Results: HTML CSV LaTeX

Showing element 2463 to 2512 of 3228 in total

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

Rank	description	red	green	network_comparison
2463	protocadherin 15 precursor. [swissprot;acc:q96qu1]	235.812	235.088	1.00308
2464	solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]
2465	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
2466	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
2467	suppressor of fused. [refseq;acc:nm_016169]
2468	zinc finger protein gli3. [swissprot;acc:p10071]
2469	limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
2470	gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
2471	zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]
2472	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748]	218.218	217.564	1.00301
2473	c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6]	218.644	217.991	1.003
2474	26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980]	216.64	217.285	1.00298
2475	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319]	218.219	217.571
2476	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	211.205	210.577
2477	mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]	216.177	216.801	1.00289
2478	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]
2479	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]	218.093	218.72	1.00287
2480	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960]
2481	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]
2482	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]
2483	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]
2484	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]
2485	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]
2486	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]
2487	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
2488	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	194.527	195.08	1.00284
2489	dc11 protein. [refseq;acc:nm_020186]
2490	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]
2491	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]
2492	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]
2493	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]
2494	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
2495	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]
2496	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]
2497	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]
2498	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]
2499	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	231.414	230.76	1.00283
2500	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	218.949	219.552	1.00275
2501	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]	217.398	216.809	1.00272
2502	adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326]	217.417	216.844	1.00264
2503	26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]	215.581	216.137	1.00258
2504	tensin. [refseq;acc:nm_022648]	218.238	217.682	1.00255
2505	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	187.853	188.326	1.00252
2506	44050 protein. [refseq;acc:nm_178832]	151.386	151.009	1.0025
2507	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]
2508	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	194.349	193.871	1.00247
2509	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	187.902	188.366
2510	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5]	234.384	234.948	1.00241
2511	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]
2512	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]

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.