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 425 to 474 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
213	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	1	210.693	186.95	1.127	
213	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [source:swissprot;acc:p07237]	0	9379.47	8436.39	1.11179	
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	1	191.644	170.192	1.12605	
214	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	0	7621.99	8473.85	1.11176	
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	1	112	126	1.125	
215	myosin vi. [source:swissprot;acc:q9um54]	0	10121.5	11250.5	1.11154	
216	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	0	10559.7	11732	1.11102	
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	1	112	126	1.125	
217	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [source:swissprot;acc:o15392]	0	7101.79	6406.18	1.10858	
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	1	112	126	1.125	
218	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	0	19355	17469.2	1.10795	
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	1	112	126	1.125	
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	1	112	126	1.125	
219	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [source:swissprot;acc:p31040]	0	12196.2	11009.7	1.10777	
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	1	112	126	1.125	
220	neurocalcin delta. [source:swissprot;acc:p29554]	0	13973.6	15473.5	1.10734	
221	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	0	12190.3	13497.2	1.10721	
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	1	112	126	1.125	
222	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	0	12183	11013.2	1.10622	
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	1	112	126	1.125	
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	1	112	126	1.125	
223	pnas-18. [source:sptrembl;acc:q9bzu3]	0	12602.7	13939.6	1.10608	
224	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [source:swissprot;acc:o76031]	0	9815.6	8889.93	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	185.969	165.623	1.12285	
225	40s ribosomal protein s29. [source:swissprot;acc:p30054]	0	11035.3	9997.71	1.10378	
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	1	226.471	201.769	1.12243	
226	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	1	239.991	269.238	1.12187	
226	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [source:swissprot;acc:p31150]	0	15395.7	16992.9	1.10374	
227	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	1	239.99	269.234	1.12186	
227	tigger transposable element derived 6. [source:refseq;acc:nm_030953]	0	12360	11200.2	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	226.411	202.088	1.12036	
228	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	0	10303.5	11370.4	1.10355	
229	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	1	226.401	202.094	1.12028	
229	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	0	10899.4	9878.1	1.10339	
230	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	1	239.35	267.915	1.11934	
230	tigger transposable element derived 7; jerky (mouse) homolog-like. [source:refseq;acc:nm_033208]	0	12364.7	11207.7	1.10323	
231	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	1	239.336	267.881	1.11927	
231	tigger transposable element derived 1; jerky (mouse) homolog-like. [source:refseq;acc:nm_145702]	0	12364.8	11207.9	1.10322	
232	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	0	12394.7	11240.2	1.10271	
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	1	239.336	267.879	1.11926	
233	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	0	9586.97	10560	1.1015	
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	1	239.32	267.842	1.11918	
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	1	287.41	256.835	1.11905	
234	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]	0	16614	18296	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	14554.5	16027.9	1.10123	
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	1	227.357	254.15	1.11785	
236	pp3111 protein. [source:refseq;acc:nm_022156]	1	227.357	254.15	1.11785	
236	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	0	15245.4	16788.5	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	9984	9067	1.10114	
237	syntaxin 18. [source:swissprot;acc:q9p2w9]	1	227.357	254.15	1.11785	

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/