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 736 to 785 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
184	small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	Squared	72886.3	98544.5	1.35203	
185	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Ranked	281.582	246.371	1.14292	
185	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Squared	41502.9	30836.8	1.34589	
185	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Measured	4069.83	5252.17	1.29051	
185	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Rooted	153.578	133.176	1.1532	
186	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Measured	4071.1	5251.75	1.29001	
186	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]	Ranked	226.582	198.444	1.14179	
186	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Squared	41502.9	30836.8	1.34589	
186	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Rooted	153.578	133.176	1.1532	
187	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Rooted	153.548	133.153	1.15317	
187	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Squared	41502.9	30836.8	1.34589	
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Ranked	226.582	198.444	1.14179	
187	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Measured	4569.48	5885.79	1.28807	
188	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Squared	41502.9	30836.8	1.34589	
188	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Ranked	226.582	198.444	1.14179	
188	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Measured	4571.89	5864.86	1.28281	
188	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Rooted	46.0352	53.0192	1.15171	
189	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Squared	41502.9	30836.8	1.34589	
189	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Measured	4571.89	5864.86	1.28281	
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Ranked	226.582	198.444	1.14179	
189	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Rooted	46.0352	53.0192	1.15171	
190	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	Squared	71389.9	96037.6	1.34525	
190	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Measured	4571.89	5864.86	1.28281	
190	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Rooted	149.165	129.699	1.15009	
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Ranked	226.582	198.444	1.14179	
191	aquaporin 5. [source:swissprot;acc:p55064]	Squared	71388.5	96035.2	1.34525	
191	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Ranked	226.582	198.444	1.14179	
191	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Rooted	63.1192	72.584	1.14995	
191	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Measured	4638.1	5923.4	1.27712	
192	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Measured	17757.5	14008	1.26767	
192	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	Squared	71387.4	96033.4	1.34524	
192	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Ranked	227.491	199.458	1.14055	
192	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Rooted	53.6107	61.5862	1.14877	
193	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	Squared	71386.9	96032.5	1.34524	
193	musashi 1. [source:refseq;acc:nm_002442]	Ranked	227.491	199.458	1.14055	
193	nostrin. [source:refseq;acc:nm_052946]	Rooted	59.6399	51.9242	1.1486	
193	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Measured	17756.5	14007.3	1.26766	
194	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	Squared	71346.6	95965.1	1.34505	
194	cyclin g2. [source:swissprot;acc:q16589]	Measured	17738.6	13995.7	1.26743	
194	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Rooted	59.6399	51.9242	1.1486	
194	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Ranked	227.491	199.458	1.14055	
195	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Measured	17738.5	13995.6	1.26743	
195	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Ranked	227.971	200.417	1.13748	
195	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Rooted	59.6399	51.9242	1.1486	
195	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	Squared	71062.4	95488.9	1.34373	
196	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	Squared	71062.4	95488.9	1.34373	
196	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Ranked	263.215	231.407	1.13745	
196	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Rooted	59.6399	51.9242	1.1486	
196	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	Measured	17738.5	13995.7	1.26742	
197	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Ranked	263.215	231.407	1.13745	

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/