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 650 to 699 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
325	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
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Divided	235.383	258.476	1.09811
341	60s ribosomal protein l9. [swissprot;acc:p32969]		240.243	263.798	1.09805
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Subtracted	240.788	261.416	20.628
342	40s ribosomal protein s20. [swissprot;acc:p17075]	Divided	243.5	267.21	1.09737
	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	Subtracted	240.913	261.45	20.537
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Divided	241.625	265.136	1.0973
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Subtracted	231.73	211.252	20.478
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Divided	241.625	265.136	1.0973
	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	Subtracted	240.6	261.041	20.441
345	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]		224.445	204.044	20.401
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Divided	242.14	265.697	1.09729
346	40s ribosomal protein s3. [swissprot;acc:p23396]		241.612	265.119
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Subtracted	231.492	211.136	20.356
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	Divided	242.14	265.697	1.09729
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Subtracted	231.481	211.131	20.35
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Divided	242.14	265.696	1.09728
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Subtracted	185.969	165.623	20.346
349	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]		255.112	234.804	20.308
	surfeit locus protein 5. [swissprot;acc:q15528]	Divided	242.14	265.696	1.09728
350	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Subtracted	233.376	253.539	20.163

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.