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 1313 to 1362 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
165	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Ranked	Divided	209.299	249.187	1.19058	
165	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Measured	Subtracted	4489.19	2765.82	1723.37	
165	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Squared	Divided	173408	242989	1.40126	
165	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Rooted	Divided	55.6486	65.1478	1.1707	
165	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Measured	Divided	23693.7	18263	1.29736	
165	musashi 1. [source:refseq;acc:nm_002442]	Rooted	Subtracted	54.9787	66.2416	11.2629	
165	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Ranked	Subtracted	133	105	28	
165	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Squared	Subtracted	59016.1	75486.9	16470.8	
166	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	Squared	Subtracted	69201.8	53013.4	16188.4	
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Ranked	Divided	209.299	249.187	1.19058	
166	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Measured	Subtracted	4489.19	2765.82	1723.37	
166	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Squared	Divided	173408	242989	1.40126	
166	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Rooted	Divided	55.6495	65.1458	1.17064	
166	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Measured	Divided	23693.7	18263	1.29736	
166	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Ranked	Subtracted	312	284	28	
166	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Rooted	Subtracted	54.9787	66.2416	11.2629	
167	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Ranked	Subtracted	133	105	28	
167	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	Squared	Subtracted	64975.9	81151.2	16175.3	
167	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]	Rooted	Subtracted	55.6161	66.7332	11.1171	
167	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Ranked	Divided	209.299	249.187	1.19058	
167	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Squared	Divided	173408	242989	1.40126	
167	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Rooted	Divided	55.65	65.1448	1.17062	
167	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Measured	Divided	23693.7	18263	1.29736	
167	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Measured	Subtracted	4489.19	2765.82	1723.37	
168	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	Squared	Subtracted	69165.6	52992.1	16173.5	
168	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Ranked	Subtracted	312	284	28	
168	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Ranked	Divided	82.5916	98.0548	1.18722	
168	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Measured	Subtracted	4489.19	2765.82	1723.37	
168	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Measured	Divided	23693.7	18263	1.29736	
168	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Squared	Divided	173408	242989	1.40126	
168	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Rooted	Subtracted	55.6161	66.7332	11.1171	
168	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Rooted	Divided	56.3709	65.8949	1.16895	
169	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Ranked	Divided	82.5916	98.0548	1.18722	
169	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Rooted	Divided	62.762	53.7761	1.1671	
169	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Ranked	Subtracted	312	284	28	
169	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Measured	Subtracted	4245.52	5942.75	1697.23	
169	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Measured	Divided	23693.7	18263	1.29736	
169	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	Squared	Subtracted	69165	52991.7	16173.3	
169	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Rooted	Subtracted	55.6161	66.7332	11.1171	
169	symplekin. [source:swissprot;acc:q92797]	Squared	Divided	124118	88668.8	1.39979	
170	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	Squared	Subtracted	69165	52991.7	16173.3	
170	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Rooted	Divided	53.4993	45.9227	1.16499	
170	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	Divided	96730.5	69286.7	1.39609	
170	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Ranked	Subtracted	227.971	200.417	27.554	
170	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Measured	Subtracted	4247.86	5941.88	1694.02	
170	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Measured	Divided	23693.7	18263	1.29736	
170	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Ranked	Divided	227.199	192.715	1.17894	
170	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Rooted	Subtracted	55.6161	66.7332	11.1171	
171	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Squared	Divided	96602.7	69211.2	1.39577	
171	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Measured	Subtracted	4117.67	5801.04	1683.37	

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/