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 green red network_comparison
Results: HTML CSV LaTeX Showing element 444 to 493 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	green	red	network_comparison	
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	1	126	112	1.125	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	1	126	112	1.125	
223	pnas-18. [source:sptrembl;acc:q9bzu3]	0	13939.6	12602.7	1.10608	
224	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [source:swissprot;acc:o76031]	0	8889.93	9815.6	1.10413	
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	1	165.623	185.969	1.12285	
225	40s ribosomal protein s29. [source:swissprot;acc:p30054]	0	9997.71	11035.3	1.10378	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	1	201.769	226.471	1.12243	
226	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	1	269.238	239.991	1.12187	
226	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [source:swissprot;acc:p31150]	0	16992.9	15395.7	1.10374	
227	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	1	269.234	239.99	1.12186	
227	tigger transposable element derived 6. [source:refseq;acc:nm_030953]	0	11200.2	12360	1.10355	
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	1	202.088	226.411	1.12036	
228	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	0	11370.4	10303.5	1.10355	
229	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	1	202.094	226.401	1.12028	
229	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	0	9878.1	10899.4	1.10339	
230	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	1	267.915	239.35	1.11934	
230	tigger transposable element derived 7; jerky (mouse) homolog-like. [source:refseq;acc:nm_033208]	0	11207.7	12364.7	1.10323	
231	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	1	267.881	239.336	1.11927	
231	tigger transposable element derived 1; jerky (mouse) homolog-like. [source:refseq;acc:nm_145702]	0	11207.9	12364.8	1.10322	
232	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	0	11240.2	12394.7	1.10271	
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	1	267.879	239.336	1.11926	
233	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	0	10560	9586.97	1.1015	
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	1	267.842	239.32	1.11918	
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	1	256.835	287.41	1.11905	
234	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]	0	18296	16614	1.10124	
235	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	0	16027.9	14554.5	1.10123	
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	1	254.15	227.357	1.11785	
236	pp3111 protein. [source:refseq;acc:nm_022156]	1	254.15	227.357	1.11785	
236	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	0	16788.5	15245.4	1.10122	
237	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	0	9067	9984	1.10114	
237	syntaxin 18. [source:swissprot;acc:q9p2w9]	1	254.15	227.357	1.11785	
238	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	0	13941.7	12677.7	1.0997	
238	rd protein. [source:swissprot;acc:p18615]	1	254.15	227.357	1.11785	
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	1	254.15	227.357	1.11785	
239	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	0	9795.36	8907.41	1.09969	
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	1	254.15	227.357	1.11785	
240	methyltransferase like 2. [source:refseq;acc:nm_018396]	0	16326	17946	1.09923	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	1	254.15	227.357	1.11785	
241	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	0	12743.3	14003.7	1.09891	
242	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	0	13895.8	15260.6	1.09822	
242	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	1	254.15	227.357	1.11785	
243	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	0	1373	1251	1.09752	
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	1	254.15	227.357	1.11785	
244	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	1	254.15	227.357	1.11785	
244	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	0	11579.9	10551.1	1.09751	
245	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	0	13019	11867.6	1.09702	
245	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	1	202.333	226.109	1.11751	
246	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	1	212.363	237.312	1.11748	
246	keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	0	11573.7	10551.6	1.09687	
247	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	0	11573.7	10551.6	1.09687	

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/