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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 1951 to 2000 of 12912 in total 
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Value Type	red	green	network_comparison	
488	secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	Squared	26866.1	32333.2	1.20349	
488	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	Ranked	225.026	209.798	1.07258	
489	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	Rooted	50.5505	46.2797	1.09228	
489	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [source:swissprot;acc:o95674]	Squared	26859	32321.2	1.20337	
489	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	Ranked	231.276	215.627	1.07257	
489	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Measured	5281.11	6044.61	1.14457	
490	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Squared	5301.97	6377.93	1.20294	
490	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Rooted	50.5505	46.2797	1.09228	
490	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [source:refseq;acc:nm_015316]	Measured	15274.9	13346.9	1.14445	
490	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	Ranked	220.183	236.015	1.0719	
491	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Squared	5302.25	6378.24	1.20293	
491	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	Measured	5980.15	6843.48	1.14437	
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	Ranked	251.83	234.951	1.07184	
491	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	Rooted	55.1759	60.2621	1.09218	
492	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Squared	5313	6389.9	1.20269	
492	hepatoma-derived growth factor-related protein 2. [source:refseq;acc:nm_032631]	Rooted	55.1759	60.2621	1.09218	
492	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Measured	5979.94	6842.76	1.14429	
492	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [source:swissprot;acc:q13177]	Ranked	220.171	235.979	1.0718	
493	cgi-142; hepatoma-derived growth factor 2. [source:refseq;acc:nm_016073]	Rooted	55.1759	60.2621	1.09218	
493	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	Ranked	220.172	235.98	1.0718	
493	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Measured	5979.95	6842.78	1.14429	
493	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [source:swissprot;acc:p21549]	Squared	28408.7	34148.5	1.20204	
494	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Measured	5979.93	6842.72	1.14428	
494	electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [source:swissprot;acc:p13804]	Squared	31583	37925.6	1.20082	
494	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [source:refseq;acc:nm_033222]	Rooted	55.1759	60.2621	1.09218	
494	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [source:swissprot;acc:q13153]	Ranked	220.172	235.98	1.0718	
495	60s ribosomal protein l8. [source:swissprot;acc:p25120]	Rooted	55.1759	60.2621	1.09218	
495	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	Squared	30286.5	36362	1.2006	
495	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [source:swissprot;acc:o75914]	Ranked	220.171	235.979	1.0718	
495	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Measured	10804.7	12363.6	1.14428	
496	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [source:swissprot;acc:p51858]	Rooted	55.1759	60.2621	1.09218	
496	nostrin. [source:refseq;acc:nm_052946]	Measured	4682.87	4093.05	1.1441	
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	Ranked	250.938	234.134	1.07177	
496	tubby protein homolog. [source:swissprot;acc:p50607]	Squared	30286.5	36362	1.2006	
497	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Measured	4682.87	4093.05	1.1441	
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	Ranked	251.344	234.514	1.07177	
497	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	Squared	30286.5	36362	1.2006	
497	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	Rooted	55.1759	60.2621	1.09218	
498	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Measured	4682.87	4093.05	1.1441	
498	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	Squared	30286.5	36362	1.2006	
498	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	Rooted	55.1759	60.2621	1.09218	
498	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [source:swissprot;acc:q15052]	Ranked	220.161	235.95	1.07172	
499	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Measured	4682.87	4093.05	1.1441	
499	rw1 protein (fragment). [source:swissprot;acc:q92545]	Rooted	55.1759	60.2621	1.09218	
499	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Squared	30286.5	36362	1.2006	
499	triosephosphate isomerase (ec 5.3.1.1) (tim). [source:swissprot;acc:p00938]	Ranked	231.496	248.048	1.0715	
500	60s ribosomal protein l7. [source:swissprot;acc:p18124]	Rooted	52.6483	48.2135	1.09198	
500	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Measured	4682.87	4093.05	1.1441	
500	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	Ranked	224.662	240.673	1.07127	
500	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Squared	30286.5	36362	1.2006	

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/