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 968 to 1017 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
484	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	Subtracted	7139.5	7994.06	854.56	
485	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	Subtracted	1881.02	1027.36	853.66	
485	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	Divided	9649.61	11053.5	1.14549	
486	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354]	Subtracted	5975.11	6826.24	851.13	
486	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Divided	10908.6	12491.8	1.14513	
487	pyrroline 5-carboxylate reductase isoform. [source:refseq;acc:nm_013328]	Divided	5277.4	6042.88	1.14505	
487	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955]	Subtracted	5975.11	6826.24	851.13	
488	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Divided	10872.4	12447	1.14483	
488	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	Subtracted	7105.27	7953.71	848.44	
489	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	Subtracted	7101.95	7949.85	847.9	
489	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Divided	5281.11	6044.61	1.14457	
490	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	Subtracted	7101.94	7949.84	847.9	
490	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [source:refseq;acc:nm_015316]	Divided	15274.9	13346.9	1.14445	
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]	Divided	5980.15	6843.48	1.14437	
491	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	Subtracted	7067.46	7909.27	841.81	
492	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Divided	5979.94	6842.76	1.14429	
492	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Subtracted	6167.93	7007.7	839.77	
493	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Subtracted	6167.93	7007.7	839.77	
493	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Divided	5979.95	6842.78	1.14429	
494	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Divided	5979.93	6842.72	1.14428	
494	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Subtracted	6167.93	7007.7	839.77	
495	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Subtracted	6167.93	7007.7	839.77	
495	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Divided	10804.7	12363.6	1.14428	
496	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Subtracted	6167.93	7007.7	839.77	
496	nostrin. [source:refseq;acc:nm_052946]	Divided	4682.87	4093.05	1.1441	
497	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Divided	4682.87	4093.05	1.1441	
497	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Subtracted	4714.85	5554.38	839.53	
498	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Divided	4682.87	4093.05	1.1441	
498	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	Subtracted	6933.17	7766.54	833.37	
499	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Divided	4682.87	4093.05	1.1441	
499	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Subtracted	6938.22	7770.65	832.43	
500	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Divided	4682.87	4093.05	1.1441	
500	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	Subtracted	10733.4	9902.6	830.8	
501	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Divided	4682.87	4093.05	1.1441	
501	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4]	Subtracted	10725.6	9896.32	829.28	
502	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	Subtracted	10719	9891.08	827.92	
502	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Divided	6913.6	7907.05	1.1437	
503	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	Subtracted	6920.69	7747.63	826.94	
503	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [source:swissprot;acc:q13625]	Divided	15182.5	13277.9	1.14344	
504	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	Subtracted	6920.71	7747.65	826.94	
504	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	Divided	10067.9	11511	1.14334	
505	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	Subtracted	6920.69	7747.63	826.94	
505	signal transduction protein cbl-b (sh3-binding protein cbl-b). [source:swissprot;acc:q13191]	Divided	6856.71	7838.3	1.14316	
506	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	Subtracted	6920.69	7747.63	826.94	
506	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Divided	3893.85	4450.98	1.14308	
507	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	Subtracted	6920.69	7747.63	826.94	
507	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [source:swissprot;acc:p22681]	Divided	6875.08	7858.38	1.14302	
508	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [source:swissprot;acc:o15120]	Divided	7556.75	8636.87	1.14293	
508	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	Subtracted	6920.69	7747.63	826.94	
509	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Divided	7551.8	8630.06	1.14278	

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/