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

Results: HTML CSV LaTeX

Showing element 5458 to 5507 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2729	ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670]	Subtracted	202.123	202.06	0.063
2730	complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021]	Divided	212.922	212.985	1.0003
		Subtracted			0.063
2731	sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]	Divided			1.0003
		Subtracted			0.063
2732	general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830]	Divided	202.233	202.175	1.00029
		Subtracted			0.058
2733	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]		219.95	220.007	0.057
	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831]	Divided	202.229	202.172	1.00028
2734	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]		219.95	220.007	1.00026
	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831]	Subtracted	202.229	202.172	0.057
2735	heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900]	Divided	220.943	220.887	1.00025
		Subtracted			0.056
2736	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	Divided	198.278	198.321	1.00022
		Subtracted			0.043
2737	transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9]	Divided			1.00022
		Subtracted			0.043
2738	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	Divided			1.00022
		Subtracted			0.043
2739	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Divided			1.00022
		Subtracted			0.043
2740	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Divided			1.00022
		Subtracted			0.043
2741	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	Divided			1.00022
		Subtracted			0.043
2742	nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494]	Divided			1.00022
		Subtracted			0.043
2743	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289]	Divided			1.00022
		Subtracted			0.043
2744	transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354]	Divided	201.476	201.514	1.00019
		Subtracted			0.038
2745	frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331]	Divided			1.00019
		Subtracted			0.038
2746	transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478]	Divided			1.00019
		Subtracted			0.038
2747	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263]	Divided	201.477		1.00018
		Subtracted			0.037
2748	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Divided	189.563	189.531	1.00017
		Subtracted			0.032
2749	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Divided	190.522	190.496	1.00014
		Subtracted			0.026
2750	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	Divided			1.00014
		Subtracted			0.026
2751	proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786]	Divided	215.338	215.312	1.00012
		Subtracted			0.026
2752	p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44]	Divided	221.7	221.716	1.00007
		Subtracted			0.016
2753	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]	Divided	208.859	208.846	1.00006
		Subtracted			0.013
2754	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914]	Divided	210.638	210.642	1.00002

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.