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

Results: HTML CSV LaTeX

Showing element 1001 to 1050 of 9634 in total

Value Type  : Ranked
Network Comparison Type  : Divided

description	Filtered	Rank	network_comparison	Interaction Map	green	red
atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p2) (atpase protein 9) (atpase subunit c). [swissprot;acc:q06055]	1	4020	1.01157	Low confidence	199.349	201.656
atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p3) (atpase protein 9) (atpase subunit c). [swissprot;acc:p48201]		4019	1.01158		199.371	201.68
atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]		456	1.07779	High confidence	226.578	210.225
		3456	1.01514	Low confidence	199.686	202.709
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]		1564	1.01648	High confidence	214.739	218.277
		3120	1.0164	Low confidence	190.14	193.258
atp-binding cassette sub-family e member 1 (rnase l inhibitor) (ribonuclease 4 inhibitor) (rns4i) (huhp68). [swissprot;acc:q96b10]		1404	1.02187		197.939	202.268
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]		2209	1.00645	High confidence	200.413	199.129
		4597	1.00727	Low confidence	203.022	204.498
atp-binding cassette, sub-family d, member 2 (adrenoleukodystrophy related protein) (haldr) (adrenoleukodystrophy-like 1). [swissprot;acc:q9ubj2]		1583	1.02104		206.669	202.41
atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288]		2166	1.00673	High confidence	214.481	215.925
		4280	1.0094	Low confidence	204.33	202.428
atp-binding cassette, sub-family f, member 2 (iron inhibited abc transporter 2) (hussy-18). [swissprot;acc:q9ug63]		1065	1.02395		196.411	201.115
atp-binding cassette, sub-family g, member 2 (placenta-specific atp- binding cassette transporter) (breast cancer resistance protein). [swissprot;acc:q9unq0]		4014	1.0116		194.242	196.496
atp-binding cassette, sub-family g, member 8 (sterolin-2). [swissprot;acc:q9h221]		4092	1.01089		200.405	202.587
atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]		2689	1.00081	High confidence	213.619	213.792
		4005	1.01168	Low confidence	199.244	201.572
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	0	224	1.10413	High confidence	8889.93	9815.6
		482	1.06127	Low confidence	11746.9	11068.7
	1	751	1.02705		196.717	202.039
		1871	1.01081	High confidence	225.228	222.819
atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	0	299	1.11945	Low confidence	11748.1	13151.4
		426	1.02805	High confidence	9676.67	9412.67
	1	2188	1.01901	Low confidence	195.391	199.106
		2727	1.00033	High confidence	220.927	221.001
atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]		2728
		2770	1.01742	Low confidence	196.644	200.069
atp-dependent dna helicase q1 (dna-dependent atpase q1). [swissprot;acc:p46063]		2148	1.01911		196.725	200.484
atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]		1703	1.01363	High confidence	219.024	216.079
		4187	1.01032	Low confidence	200.37	202.438
atp-dependent helicase ddx8 (rna helicase hrh1) (deah-box protein 8). [swissprot;acc:q14562]		691	1.02806		196.158	201.663
atp-dependent rna helicase a (nuclear dna helicase ii) (ndh ii) (dead-box protein 9). [swissprot;acc:q08211]		4749	1.00525		207.793	208.883
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]		529	1.06856	High confidence	235.506	251.653
		1148	1.02342	Low confidence	195.785	200.371
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]		328	1.09888	High confidence	235.183	258.437
		587	1.03048	Low confidence	199.383	205.461
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]		428	1.0811	High confidence	234.808	253.852
		682	1.02819	Low confidence	198.663	204.263
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]		990	1.03367	High confidence	235.373	243.297
		1837	1.01996	Low confidence	201.012	205.024
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]		1365	1.02194	High confidence	223.736	228.644
		3157	1.01623	Low confidence	198.963	202.193
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]		1126	1.02742	High confidence	212.656	218.487
		2103	1.01924	Low confidence	193.327	197.046
atpase, h+ transporting, lysosomal 42kda, v1 subunit c isoform 2; v-atpase c2 subunit. [refseq;acc:nm_144583]		787	1.02651		197.259	202.489
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]		1120	1.02752	High confidence	212.676	218.528
		1162	1.02331	Low confidence	187.907	192.287
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]		1384	1.02148	High confidence	213.876	218.471
		1438	1.0217	Low confidence	198.892	203.208
atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]		1035	1.03157	High confidence	228.68	221.682

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.