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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
251	40s ribosomal protein s20. [source:swissprot;acc:p17075]	Subtracted	243.5	267.21	23.71	
251	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Divided	186.172	166.661	1.11707	
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Divided	237.292	212.457	1.11689	
252	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Subtracted	228	204.333	23.667	
253	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Divided	228	204.333	1.11583	
253	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	Subtracted	251.679	228.037	23.642	
254	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Subtracted	227.999	204.357	23.642	
254	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Divided	200.691	179.88	1.11569	
255	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Subtracted	227.999	204.366	23.633	
255	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Divided	200.691	179.88	1.11569	
256	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Subtracted	227.999	204.37	23.629	
256	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Divided	227.999	204.357	1.11569	
257	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]	Divided	200.691	179.88	1.11569	
257	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	Subtracted	242.14	265.697	23.557	
258	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	Subtracted	242.14	265.697	23.557	
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Divided	227.999	204.366	1.11564	
259	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	Subtracted	242.14	265.696	23.556	
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Divided	227.999	204.37	1.11562	
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Divided	219.421	196.978	1.11394	
260	surfeit locus protein 5. [source:swissprot;acc:q15528]	Subtracted	242.14	265.696	23.556	
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Divided	219.421	196.978	1.11394	
261	zinc finger protein 291. [source:swissprot;acc:q9by12]	Subtracted	242.14	265.696	23.556	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Divided	219.421	196.978	1.11394	
262	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	Subtracted	242.14	265.696	23.556	
263	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Divided	219.421	196.978	1.11394	
263	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Subtracted	242.14	265.696	23.556	
264	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Subtracted	243.24	266.796	23.556	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Divided	219.421	196.978	1.11394	
265	60s ribosomal protein l9. [source:swissprot;acc:p32969]	Subtracted	240.243	263.798	23.555	
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Divided	225.217	202.459	1.11241	
266	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Subtracted	243.12	266.662	23.542	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Divided	241.07	267.88	1.11121	
267	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Subtracted	243.12	266.661	23.541	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Divided	241.07	267.88	1.11121	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Divided	271.016	244.167	1.10996	
268	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Subtracted	241.625	265.136	23.511	
269	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Subtracted	241.625	265.136	23.511	
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Divided	241.373	267.352	1.10763	
270	40s ribosomal protein s3. [source:swissprot;acc:p23396]	Subtracted	241.612	265.119	23.507	
270	fad synthetase. [source:refseq;acc:nm_025207]	Divided	241.373	267.352	1.10763	
271	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]	Divided	241.373	267.352	1.10763	
271	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	Subtracted	243.072	266.559	23.487	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Divided	241.373	267.352	1.10763	
272	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	Subtracted	242.83	266.248	23.418	
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252]	Divided	241.373	267.352	1.10763	
273	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Subtracted	243.208	266.617	23.409	
274	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	Subtracted	242.744	266.07	23.326	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Divided	241.373	267.352	1.10763	
275	40s ribosomal protein s5. [source:swissprot;acc:p46782]	Subtracted	242.473	265.756	23.283	
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Divided	241.373	267.352	1.10763	

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/