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 863 to 912 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
108	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4]	Rooted	Subtracted	63.7475	48.1615	15.586	
108	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	Rooted	Divided	49.2925	62.397	1.26585	
109	44050 protein. [source:refseq;acc:nm_178832]	Measured	Subtracted	17385.9	14889.2	2496.7	
109	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Squared	Subtracted	88432.6	58423.3	30009.3	
109	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Ranked	Subtracted	209.299	249.187	39.888	
109	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Ranked	Divided	266.933	333.281	1.24856	
109	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Squared	Divided	19321	12542.6	1.54043	
109	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Rooted	Subtracted	30.8986	46.4619	15.5633	
109	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Measured	Divided	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	Divided	49.2923	62.3969	1.26585	
110	deltex 2. [source:refseq;acc:nm_020892]	Ranked	Divided	333.144	267.393	1.2459	
110	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Ranked	Subtracted	209.299	249.187	39.888	
110	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Rooted	Subtracted	33.9632	18.4255	15.5377	
110	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Squared	Divided	19321	12542.6	1.54043	
110	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	Measured	Subtracted	17385.9	14889.2	2496.7	
110	pnas-18. [source:sptrembl;acc:q9bzu3]	Squared	Subtracted	87787.3	58155.8	29631.5	
110	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Measured	Divided	4366.44	5899.76	1.35116	
110	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Rooted	Divided	49.293	62.3973	1.26585	
111	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Squared	Subtracted	79779.8	108084	28304.2	
111	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Ranked	Divided	332.925	267.274	1.24563	
111	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Ranked	Subtracted	209.299	249.187	39.888	
111	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Rooted	Subtracted	33.9632	18.4255	15.5377	
111	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Squared	Divided	19321	12542.6	1.54043	
111	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Measured	Divided	4366.44	5899.76	1.35116	
111	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	Measured	Subtracted	12365.2	14824.9	2459.7	
111	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Rooted	Divided	49.2923	62.3969	1.26585	
112	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	Measured	Subtracted	11757.8	9352.11	2405.69	
112	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [source:refseq;acc:nm_019857]	Squared	Subtracted	96730.5	69286.7	27443.8	
112	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Ranked	Subtracted	275.754	235.908	39.846	
112	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Squared	Divided	19321	12542.6	1.54043	
112	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Rooted	Subtracted	33.9632	18.4255	15.5377	
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	Divided	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	Divided	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	Divided	49.3267	62.4167	1.26537	
113	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Rooted	Divided	80.4705	101.526	1.26165	
113	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Squared	Subtracted	96602.7	69211.2	27391.5	
113	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Measured	Subtracted	4800.81	7132.71	2331.9	
113	db83 protein. [source:swissprot;acc:p57088]	Rooted	Subtracted	33.9632	18.4255	15.5377	
113	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Measured	Divided	4366.44	5899.76	1.35116	
113	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Ranked	Divided	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	Divided	19321	12542.6	1.54043	
113	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Ranked	Subtracted	194.372	234.204	39.832	
114	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	Squared	Subtracted	67438.6	40697	26741.6	
114	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Ranked	Subtracted	229.818	267.265	37.447	
114	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Rooted	Divided	80.4705	101.526	1.26165	
114	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Measured	Subtracted	13768.2	11466	2302.2	
114	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	Rooted	Subtracted	40.225	24.7051	15.5199	
114	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Measured	Divided	4300.47	5807.72	1.35048	
114	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Ranked	Divided	332.874	267.246	1.24557	
114	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Squared	Divided	19321	12542.6	1.54043	

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/