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

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Showing element 501 to 550 of 9634 in total

Value Type  : Ranked
Network Comparison Type  : Divided

description	Rank	green	Interaction Map	Filtered	network_comparison	red
actin-related protein 6 (harp6) (harpx) (cda12). [swissprot;acc:q9gzn1]	3049	196.826	Low confidence	1	1.0166	200.094
actin-related protein 8. [swissprot;acc:q9h981]	4788	213.795			1.00435	212.869
activated p21cdc42hs kinase. [refseq;acc:nm_005781]	493	202.478			1.03288	209.136
	2341	230.294	High confidence		1.00452	229.258
activated rna polymerase ii transcriptional coactivator p15 (pc4) (p14). [swissprot;acc:p53999]	3118	198.391	Low confidence		1.01641	201.646
activator 1 140 kda subunit (replication factor c large subunit) (a1 140 kda subunit) (rf-c 140 kda subunit) (activator 1 large subunit) (dna-binding protein po-ga). [swissprot;acc:p35251]	2771	197.788			1.01742	201.233
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]	1169	213.784	High confidence		1.02626	219.399
	2633	199.198	Low confidence		1.01778	202.74
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482]	1303	275.531	High confidence		1.02368	269.157
	4902	208.323	Low confidence		1.00197	208.733
activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	1257	199.543			1.02259	204.05
	1366	228.795	High confidence		1.02194	223.884
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]	2874	200.634	Low confidence		1.01711	204.066
	3050	0.00001	High confidence		1	0.00001
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]	2498	195.08			1.00284	194.527
	2823	193.252	Low confidence		1.01725	196.586
acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	1413	210.42	High confidence		1.02095	206.102
	1757	198.864	Low confidence		1.02029	202.898
acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	105	14360	High confidence	0	1.21243	17410.5
	655	14410	Low confidence		1.02356	14078.3
	2019	213.865	High confidence	1	1.00904	215.799
	3051	199.311	Low confidence		1.01659	202.617
acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	733	155.961	High confidence		1.05154	164
	853	194.759	Low confidence		1.02582	199.788
acyl-coa desaturase (ec 1.14.19.1) (stearoyl-coa desaturase) (fatty acid desaturase) (delta(9)-desaturase). [swissprot;acc:o00767]	4723	195.824			1.00555	196.91
acyl-coa-binding protein (acbp) (diazepam binding inhibitor) (dbi) (endozepine) (ep). [swissprot;acc:p07108]	1698	197.873			1.02056	201.941
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]	1697
	2643	194.328	High confidence		1.00119	194.097
acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424]	2404	194.105			1.0037	193.389
	2754	193.162	Low confidence		1.01745	196.532
acyl-coenzyme a oxidase 3, peroxisomal (ec 1.3.3.6) (pristanoyl-coa oxidase). [swissprot;acc:o15254]	3892	197.485			1.01271	199.996
ad-003 protein. [refseq;acc:nm_014064]	3670	200.281			1.0139	203.065
ad023 protein. [refseq;acc:nm_020679]	3422	199.025			1.01523	202.056
ad037 protein isoform a. [refseq;acc:nm_032023]	4059	200.731			1.01123	202.985
ad24 protein. [refseq;acc:nm_022451]	505	234.672	High confidence		1.071	251.334
	947	198.533	Low confidence		1.02488	203.472
adam-ts related protein 1 isoform 1; adam-ts related protein 1; thrombospondin; punctin. [refseq;acc:nm_139238]	1620	199.732			1.02083	203.893
adam-tsl3 precursor (fragment). [sptrembl;acc:p82987]	1623	199.748			1.0208	203.903
adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]	2481	199.724			1.01825	203.369
	2516	216.341	High confidence		1.00234	215.835
adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567]	458	200.058	Low confidence		1.03444	206.948
	1586	225.79	High confidence		1.01631	222.166
adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747]	416	200.339	Low confidence		1.03545	207.442
	1596	225.731	High confidence		1.01619	222.134
adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843]	408	200.363	Low confidence		1.03591	207.558
	1594	225.731	High confidence		1.0162	222.133
adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382]	699	199.601	Low confidence		1.0279	205.169
	1598	225.731	High confidence		1.01619	222.134
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	368	15940.6		0	1.04633	16679.2
	565	13171.2	Low confidence		1.04452	12609.8

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.