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 277 to 326 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
139	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Divided	271.752	225.68	1.20415	
139	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Subtracted	287.41	256.835	30.575	
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Subtracted	228.306	198.011	30.295	
140	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Divided	59	49	1.20408	
141	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Subtracted	239.991	269.238	29.247	
141	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Divided	59	49	1.20408	
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Divided	59	49	1.20408	
142	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Subtracted	239.99	269.234	29.244	
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Divided	59	49	1.20408	
143	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Subtracted	240.133	211.382	28.751	
144	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Subtracted	239.35	267.915	28.565	
144	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Divided	265.686	319.651	1.20312	
145	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Subtracted	239.336	267.881	28.545	
145	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Divided	265.639	319.546	1.20293	
146	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Divided	265.632	319.531	1.20291	
146	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Subtracted	239.336	267.879	28.543	
147	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	Subtracted	239.32	267.842	28.522	
147	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Divided	50.7983	42.3003	1.2009	
148	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]	Subtracted	226.582	198.444	28.138	
148	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Divided	296.677	247.559	1.19841	
149	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Divided	142	170	1.19718	
149	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Subtracted	226.582	198.444	28.138	
150	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Divided	55	46	1.19565	
150	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Subtracted	226.582	198.444	28.138	
151	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Divided	55	46	1.19565	
151	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Subtracted	226.582	198.444	28.138	
152	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Divided	55	46	1.19565	
152	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Subtracted	226.582	198.444	28.138	
153	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Divided	249.663	298.263	1.19466	
153	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Subtracted	226.582	198.444	28.138	
154	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Subtracted	227.491	199.458	28.033	
154	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	Divided	249.663	298.263	1.19466	
155	musashi 1. [source:refseq;acc:nm_002442]	Subtracted	227.491	199.458	28.033	
155	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	Divided	249.663	298.263	1.19466	
156	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Subtracted	227.491	199.458	28.033	
156	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [source:swissprot;acc:o76081]	Divided	249.663	298.263	1.19466	
157	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Subtracted	312	284	28	
157	transcription factor lbx1. [source:swissprot;acc:p52954]	Divided	249.663	298.263	1.19466	
158	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Subtracted	312	284	28	
158	mosaic protein lgn. [source:swissprot;acc:p81274]	Divided	249.663	298.263	1.19466	
159	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Subtracted	312	284	28	
159	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	Divided	249.663	298.263	1.19466	
160	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	Divided	249.663	298.263	1.19466	
160	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Subtracted	312	284	28	
161	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Subtracted	312	284	28	
161	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Divided	249.663	298.263	1.19466	
162	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Subtracted	142	170	28	
162	nostrin. [source:refseq;acc:nm_052946]	Divided	209.299	249.187	1.19058	
163	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Subtracted	133	105	28	
163	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Divided	209.299	249.187	1.19058	

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/