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 475 to 524 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
238	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Subtracted	252.512	228.356	24.156	
238	rd protein. [source:swissprot;acc:p18615]	Divided	227.357	254.15	1.11785	
239	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	Subtracted	243.817	267.962	24.145	
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	Divided	227.357	254.15	1.11785	
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	Divided	227.357	254.15	1.11785	
240	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Subtracted	252.39	228.297	24.093	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	Divided	227.357	254.15	1.11785	
241	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	Subtracted	241.892	265.96	24.068	
242	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Subtracted	241.892	265.959	24.067	
242	j domain containing protein 1. [source:swissprot;acc:q9ukb3]	Divided	227.357	254.15	1.11785	
243	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Subtracted	241.884	265.945	24.061	
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [source:swissprot;acc:q9y5w8]	Divided	227.357	254.15	1.11785	
244	60s ribosomal protein l5. [source:swissprot;acc:p46777]	Subtracted	241.899	265.924	24.025	
244	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	Divided	227.357	254.15	1.11785	
245	60s ribosomal protein l19. [source:swissprot;acc:p14118]	Subtracted	240.73	264.729	23.999	
245	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Divided	226.109	202.333	1.11751	
246	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Subtracted	243.583	267.528	23.945	
246	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Divided	237.312	212.363	1.11748	
247	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Subtracted	243.583	267.527	23.944	
247	rna-binding protein. [source:refseq;acc:nm_019027]	Divided	237.302	212.41	1.11719	
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Divided	237.302	212.41	1.11719	
248	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	Subtracted	243.583	267.527	23.944	
249	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Divided	237.302	212.41	1.11719	
249	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Subtracted	226.109	202.333	23.776	
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Divided	237.302	212.41	1.11719	
250	pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	Subtracted	210.693	186.95	23.743	
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	

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/