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

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Showing element 630 to 679 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
315	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Divided	244.126	268.604	1.10027
316	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Subtracted	88.2482	110.265	22.0168
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Divided	242.694	267.017	1.10022
317	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Subtracted	88.2482	110.265	22.0168
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Divided	224.445	204.044	1.09998
318	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Subtracted	88.2482	110.265	22.0168
	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Divided	242.011	266.18	1.09987
319	60s ribosomal protein l19. [swissprot;acc:p14118]		240.73	264.729	1.09969
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Subtracted	88.2482	110.265	22.0168
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Divided	241.892	265.96	1.0995
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Subtracted	88.2482	110.265	22.0168
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Divided	241.892	265.959	1.09949
	trophinin. [swissprot;acc:q12816]	Subtracted	88.2482	110.265	22.0168
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Divided	86.7483	78.8995	1.09948
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Subtracted	231.969	210.064	21.905
323	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]		242.238	264.11	21.872
	60s ribosomal protein l23a. [swissprot;acc:p29316]	Divided	241.884	265.945	1.09947
324	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Subtracted	242.238	264.11	21.872
	40s ribosomal protein s23. [swissprot;acc:p39028]	Divided	243.944	268.195	1.09941
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	Subtracted	241.828	263.62	21.792
326	40s ribosomal protein s16. [swissprot;acc:p17008]
	60s ribosomal protein l5. [swissprot;acc:p46777]	Divided	241.899	265.924	1.09932
327	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	Subtracted	241.83	263.615	21.785
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Divided	243.817	267.962	1.09903
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]		258.437	235.183	1.09888
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Subtracted	240.801	262.34	21.539
329	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		191.644	170.192	21.452
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Divided	312	284	1.09859
330	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	Subtracted	224.657	203.235	21.422
331	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Divided	312	284	1.09859
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Subtracted	224.647	203.242	21.405
332	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]		224.633	203.251	21.382
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Divided	312	284	1.09859
333	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Subtracted	265.634	244.304	21.33
334	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Divided	312	284	1.09859
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Subtracted	232.473	211.207	21.266
335	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Divided	312	284	1.09859
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Subtracted	223.273	202.423	20.85
336	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Divided	312	284	1.09859
	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Subtracted	241.045	261.874	20.829
337	60s ribosomal protein l12. [swissprot;acc:p30050]	Divided	243.583	267.527	1.0983
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Subtracted	200.691	179.88	20.811
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Divided	243.583	267.528	1.0983
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Subtracted	200.691	179.88	20.811
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Divided	243.583	267.527	1.0983
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Subtracted	200.691	179.88	20.811
340	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		239.75	260.544	20.794

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.