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

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Showing element 4958 to 5007 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2479	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]	Divided	218.093	218.72	1.00287
2480	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]	Subtracted			0.627
	rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960]	Divided			1.00287
2481	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]
	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]	Subtracted			0.627
2482	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]	Divided			1.00287
	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]	Subtracted			0.627
2483	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]	Divided			1.00287
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Subtracted			0.627
2484	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]	Divided			1.00287
2485	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]
	mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212]	Subtracted	216.177	216.801	0.624
2486	26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Divided	218.093	218.72	1.00287
2487	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Subtracted	218.949	219.552	0.603
	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]	Divided	218.093	218.72	1.00287
2488	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804]	Subtracted	180.137	180.732	0.595
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Divided	194.527	195.08	1.00284
2489	dc11 protein. [refseq;acc:nm_020186]
	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]	Subtracted	182.272	181.683	0.589
2490	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]	Divided	194.527	195.08	1.00284
	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]	Subtracted	217.398	216.809	0.589
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]	Divided	194.527	195.08	1.00284
	adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326]	Subtracted	217.417	216.844	0.573
2492	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5]		234.384	234.948	0.564
	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	Divided	194.527	195.08	1.00284
2493	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]	Subtracted	234.384	234.948	0.564
	ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314]	Divided	194.527	195.08	1.00284
2494	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
	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]	Subtracted	234.384	234.948	0.564
2495	melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]	Divided	194.527	195.08	1.00284
	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]	Subtracted	234.384	234.948	0.564
2496	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	Divided	194.527	195.08	1.00284
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Subtracted	234.384	234.948	0.564
2497	26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]		215.581	216.137	0.556
	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0]	Divided	194.527	195.08	1.00284
2498	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]
	tensin. [refseq;acc:nm_022648]	Subtracted	218.238	217.682	0.556
2499	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]		194.527	195.08	0.553
	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	Divided	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
	dc11 protein. [refseq;acc:nm_020186]	Subtracted	194.527	195.08	0.553
2501	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]
	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]	Divided	217.398	216.809	1.00272
2502	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557]	Subtracted	194.527	195.08	0.553
	adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326]	Divided	217.417	216.844	1.00264
2503	26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527]		215.581	216.137	1.00258
	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	Subtracted	194.527	195.08	0.553
2504	tensin. [refseq;acc:nm_022648]	Divided	218.238	217.682	1.00255

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.