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	network_comparison	green

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Showing element 2725 to 2774 of 3228 in total

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

Rank	description	red	network_comparison	green
2725	doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602]	216.496	1.00034	216.569
2726	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	221.001	1.00033	220.927
2727	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]
2728	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]
2729	ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670]	202.123	1.00031	202.06
2730	complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021]	212.922	1.0003	212.985
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]
2732	general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830]	202.233	1.00029	202.175
2733	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831]	202.229	1.00028	202.172
2734	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	219.95	1.00026	220.007
2735	heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900]	220.943	1.00025	220.887
2736	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	198.278	1.00022	198.321
2737	transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9]
2738	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]
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]
2740	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]
2741	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]
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]
2743	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289]
2744	transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354]	201.476	1.00019	201.514
2745	frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331]
2746	transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478]
2747	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263]	201.477	1.00018
2748	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	189.563	1.00017	189.531
2749	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	190.522	1.00014	190.496
2750	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]
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]	215.338	1.00012	215.312
2752	p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44]	221.7	1.00007	221.716
2753	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]	208.859	1.00006	208.846
2754	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914]	210.638	1.00002	210.642
2755	deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366]	212.403	1.00001	212.401
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0.00001	1	0.00001
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
2759	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]
2762	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
2763	ring finger protein 3. [refseq;acc:nm_006315]
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
2765	histone h2a.e (h2a/e). [swissprot;acc:q99878]
2766	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
2768	histone h2a.x (h2a/x). [swissprot;acc:p16104]
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
2770	nipsnap1 protein. [swissprot;acc:q9bpw8]
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
2772	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
2774	dc12 protein. [refseq;acc:nm_020187]

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.