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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 294 to 343 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
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	
164	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Subtracted	133	105	28	
164	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Divided	209.299	249.187	1.19058	
165	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Divided	209.299	249.187	1.19058	
165	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Subtracted	133	105	28	
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Divided	209.299	249.187	1.19058	
166	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Subtracted	312	284	28	
167	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Subtracted	133	105	28	
167	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Divided	209.299	249.187	1.19058	
168	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Subtracted	312	284	28	
168	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Divided	82.5916	98.0548	1.18722	
169	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Divided	82.5916	98.0548	1.18722	
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]	Subtracted	312	284	28	
170	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Subtracted	227.971	200.417	27.554	
170	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Divided	227.199	192.715	1.17894	
171	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Divided	227.202	192.823	1.17829	
171	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Subtracted	201.478	228.784	27.306	
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	Divided	174.667	205.556	1.17685	

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/