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

Results: HTML CSV LaTeX

Showing element 501 to 550 of 9634 in total

Value Type  : Ranked
Network Comparison Type  : Divided

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

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.