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

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Showing element 644 to 693 of 3228 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided

Rank	description	green	red	network_comparison
644	cgthba protein (-14 gene protein). [swissprot;acc:q12980]	230.596	217.67	1.05938
645	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
646	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	229.549	216.731	1.05914
647	dynein light chain 2. [refseq;acc:nm_080677]
648	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	206.078	218.227	1.05895
649	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	220.751	233.725	1.05877
650	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	216.276	228.986
651	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	220.751	233.725
652	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	235.255	248.994	1.0584
653	dok-like protein. [refseq;acc:nm_024872]	204.622	216.504	1.05807
654	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]
655	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
656	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]
657	synapsin iii. [swissprot;acc:o14994]	216.576	229.072	1.0577
658	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
659	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]
660	actin binding lim protein 2. [refseq;acc:nm_032432]
661	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
662	synapsin ii. [swissprot;acc:q92777]
663	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
664	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
665	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
666	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
669	synapsin i (brain protein 4.1). [swissprot;acc:p17600]
670	autoantigen ngp-1. [swissprot;acc:q13823]	236.817	250.302	1.05694
671	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	199.398	210.739	1.05688
672	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
673	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	214.355	226.497	1.05664
674	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]
675	single-minded homolog 1. [swissprot;acc:p81133]
676	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	245.613	232.469	1.05654
677	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	216.745	228.944	1.05628
678	sorting nexin 5. [swissprot;acc:q9y5x3]	220.175	208.482	1.05609
679	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	125.389	132.413	1.05602
680	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]
681	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
683	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]
684	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
685	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
687	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	250.823	237.554	1.05586
689	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	128.225	135.379	1.05579
690	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	208.987	220.593	1.05553
691	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	206.195	217.602	1.05532
692	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
693	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	234.847	222.554	1.05524

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.