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

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Showing element 662 to 711 of 3228 in total

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

Rank	green	description	network_comparison	red
662	216.576	synapsin ii. [swissprot;acc:q92777]	1.0577	229.072
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	236.817	autoantigen ngp-1. [swissprot;acc:q13823]	1.05694	250.302
671	199.398	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	1.05688	210.739
672		nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
673	214.355	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	1.05664	226.497
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	245.613	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	1.05654	232.469
677	216.745	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	1.05628	228.944
678	220.175	sorting nexin 5. [swissprot;acc:q9y5x3]	1.05609	208.482
679	125.389	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.05602	132.413
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	250.823	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	1.05586	237.554
689	128.225	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	1.05579	135.379
690	208.987	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	1.05553	220.593
691	206.195	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	1.05532	217.602
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	234.847	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]	1.05524	222.554
694	229.35	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	1.05475	241.907
695	214.405	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	1.05471	226.135
696	213.64	sr rich protein. [refseq;acc:nm_032870]	1.05455	225.293
697	209.113	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	1.05419	220.444
698	209.118	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	1.05413	220.437
699		cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]		220.438
700		dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
701		disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]
702		putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]
703		limkain b1. [refseq;acc:nm_019081]
704		putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
705		cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
706		disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]
707		kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]
708		disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
709		ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]
710		disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
711	245.048	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	1.05411	232.468

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.