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

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Showing element 501 to 550 of 9634 in total

Value Type  : Ranked
Network Comparison Type  : Divided

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