Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 858 to 907 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
108	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	Rooted	0	13.7191	17.6786	1.28861	
108	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Measured	1	4366.44	5899.76	1.35116	
108	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Ranked	1	252.296	201.995	1.24902	
108	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Squared	1	19321	12542.6	1.54043	
108	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Ranked	0	10585.3	12769.1	1.2063	
108	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [source:swissprot;acc:q13813]	Squared	0	795.24	1645.86	2.06964	
108	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	Rooted	1	49.2925	62.397	1.26585	
109	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Measured	0	100	144	1.44	
109	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	Ranked	0	14466.8	12031.7	1.20239	
109	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Ranked	1	266.933	333.281	1.24856	
109	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Squared	1	19321	12542.6	1.54043	
109	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [source:swissprot;acc:q96jq0]	Rooted	0	2.64575	3.38392	1.279	
109	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Measured	1	4366.44	5899.76	1.35116	
109	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	Rooted	1	49.2923	62.3969	1.26585	
109	williams-beuren syndrome critical region protein 20 copy b. [source:refseq;acc:nm_145645]	Squared	0	16.4056	33.4891	2.04132	
110	deltex 2. [source:refseq;acc:nm_020892]	Ranked	1	333.144	267.393	1.2459	
110	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Ranked	0	12584.5	10470.6	1.20189	
110	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Squared	1	19321	12542.6	1.54043	
110	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Measured	1	4366.44	5899.76	1.35116	
110	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Rooted	0	7.7419	6.06104	1.27732	
110	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [source:swissprot;acc:q13813]	Measured	0	1833	2637	1.43863	
110	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Rooted	1	49.293	62.3973	1.26585	
110	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [source:refseq;acc:nm_018044]	Squared	0	16.4056	33.4891	2.04132	
111	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Ranked	1	332.925	267.274	1.24563	
111	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Squared	1	19321	12542.6	1.54043	
111	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Measured	1	4366.44	5899.76	1.35116	
111	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	Ranked	0	9940.69	11929	1.20002	
111	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Measured	0	2965.5	2063	1.43747	
111	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	Rooted	0	21.0524	16.4963	1.27619	
111	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Rooted	1	49.2923	62.3969	1.26585	
111	williams beuren syndrome chromosome region 20c isoform 1. [source:refseq;acc:nm_032158]	Squared	0	16.4056	33.4891	2.04132	
112	40s ribosomal protein s26. [source:swissprot;acc:p02383]	Ranked	0	14269.7	17098	1.1982	
112	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [source:swissprot;acc:q9uiv1]	Rooted	0	22.4608	17.665	1.27149	
112	lats homolog 1. [source:refseq;acc:nm_004690]	Measured	0	160	112.25	1.42539	
112	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	Squared	0	138.269	68.9705	2.00476	
112	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Squared	1	19321	12542.6	1.54043	
112	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Ranked	1	332.874	267.246	1.24557	
112	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Measured	1	4366.44	5899.76	1.35116	
112	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Rooted	1	49.3267	62.4167	1.26537	
113	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Rooted	1	80.4705	101.526	1.26165	
113	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Measured	1	4366.44	5899.76	1.35116	
113	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	Squared	0	387.336	770.962	1.99042	
113	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Ranked	1	332.874	267.246	1.24557	
113	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Squared	1	19321	12542.6	1.54043	
113	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Rooted	0	72.1137	56.7758	1.27015	
113	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Ranked	0	5673.33	6797.56	1.19816	
113	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [source:swissprot;acc:q9ujc5]	Measured	0	160	112.25	1.42539	
114	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Rooted	1	80.4705	101.526	1.26165	
114	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	Ranked	0	8871.11	10603.2	1.19525	
114	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Measured	0	671.769	472.945	1.4204	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/