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

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 873 to 922 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
110	deltex 2. [refseq;acc:nm_020892]	Ranked	1	333.144	267.393	1.2459
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Ranked	0	12584.5	10470.6	1.20189
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Squared	1	19321	12542.6	1.54043
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Measured	1	4366.44	5899.76	1.35116
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Rooted	0	7.7419	6.06104	1.27732
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Measured	0	1833	2637	1.43863
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Rooted	1	49.293	62.3973	1.26585
	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. [refseq;acc:nm_018044]	Squared	0	16.4056	33.4891	2.04132
111	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Ranked	1	332.925	267.274	1.24563
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Squared		19321	12542.6	1.54043
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Measured		4366.44	5899.76	1.35116
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Ranked	0	9940.69	11929	1.20002
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured		2965.5	2063	1.43747
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Rooted		21.0524	16.4963	1.27619
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Rooted	1	49.2923	62.3969	1.26585
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	Squared	0	16.4056	33.4891	2.04132
112	40s ribosomal protein s26. [swissprot;acc:p02383]	Ranked		14269.7	17098	1.1982
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Rooted		22.4608	17.665	1.27149
	lats homolog 1. [refseq;acc:nm_004690]	Measured		160	112.25	1.42539
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Squared		138.269	68.9705	2.00476
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Squared	1	19321	12542.6	1.54043
	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Ranked		332.874	267.246	1.24557
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Measured		4366.44	5899.76	1.35116
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Rooted		49.3267	62.4167	1.26537
113	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Rooted		80.4705	101.526	1.26165
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Measured		4366.44	5899.76	1.35116
	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	Squared	0	387.336	770.962	1.99042
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Ranked	1	332.874	267.246	1.24557
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Squared	1	19321	12542.6	1.54043
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Rooted	0	72.1137	56.7758	1.27015
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Ranked		5673.33	6797.56	1.19816
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Measured		160	112.25	1.42539
114	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Rooted	1	80.4705	101.526	1.26165
	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	Ranked	0	8871.11	10603.2	1.19525
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	Measured	0	671.769	472.945	1.4204
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Measured	1	4300.47	5807.72	1.35048
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Ranked		332.874	267.246	1.24557
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Squared		19321	12542.6	1.54043
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Rooted	0	14.7363	18.7165	1.27009
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Squared	0	35.0828	69.7867	1.9892
115	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured	1	21185	28492	1.34491
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Squared	0	105.615	53.4024	1.97772
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Squared	1	19321	12542.6	1.54043
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Rooted	0	18.4959	14.5738	1.26912
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Ranked	1	332.874	267.246	1.24557
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Rooted	1	80.4705	101.526	1.26165
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Ranked	0	18662.8	15627	1.19427
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Measured		385	543	1.41039
116	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Measured		668	475	1.40632
116	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Rooted	1	80.4705	101.526	1.26165

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.

- http://analysis.yellowcouch.org/