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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 644 to 693 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
322	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Subtracted	210.064	231.969	21.905
323	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]		264.11	242.238	21.872
	60s ribosomal protein l23a. [swissprot;acc:p29316]	Divided	265.945	241.884	1.09947
324	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Subtracted	264.11	242.238	21.872
	40s ribosomal protein s23. [swissprot;acc:p39028]	Divided	268.195	243.944	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	263.62	241.828	21.792
326	40s ribosomal protein s16. [swissprot;acc:p17008]
	60s ribosomal protein l5. [swissprot;acc:p46777]	Divided	265.924	241.899	1.09932
327	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	Subtracted	263.615	241.83	21.785
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Divided	267.962	243.817	1.09903
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]		235.183	258.437	1.09888
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Subtracted	262.34	240.801	21.539
329	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		170.192	191.644	21.452
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Divided	284	312	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	203.235	224.657	21.422
331	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Divided	284	312	1.09859
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Subtracted	203.242	224.647	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]		203.251	224.633	21.382
	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Divided	284	312	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	244.304	265.634	21.33
334	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Divided	284	312	1.09859
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Subtracted	211.207	232.473	21.266
335	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Divided	284	312	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	202.423	223.273	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	284	312	1.09859
	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Subtracted	261.874	241.045	20.829
337	60s ribosomal protein l12. [swissprot;acc:p30050]	Divided	267.527	243.583	1.0983
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Subtracted	179.88	200.691	20.811
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Divided	267.528	243.583	1.0983
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Subtracted	179.88	200.691	20.811
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Divided	267.527	243.583	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	179.88	200.691	20.811
340	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		260.544	239.75	20.794
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Divided	258.476	235.383	1.09811
341	60s ribosomal protein l9. [swissprot;acc:p32969]		263.798	240.243	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	261.416	240.788	20.628
342	40s ribosomal protein s20. [swissprot;acc:p17075]	Divided	267.21	243.5	1.09737
	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	Subtracted	261.45	240.913	20.537
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Divided	265.136	241.625	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	211.252	231.73	20.478
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Divided	265.136	241.625	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	261.041	240.6	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]		204.044	224.445	20.401
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Divided	265.697	242.14	1.09729
346	40s ribosomal protein s3. [swissprot;acc:p23396]		265.119	241.612
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Subtracted	211.136	231.492	20.356
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	Divided	265.697	242.14	1.09729

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.