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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 497 to 546 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
249	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	0	10551.6	11573.7	1.09687	
249	ns1-associated protein 1. [source:refseq;acc:nm_006372]	1	237.302	212.41	1.11719	
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	1	237.302	212.41	1.11719	
250	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	0	10551.6	11573.7	1.09687	
251	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	0	10551.6	11573.6	1.09686	
251	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	1	186.172	166.661	1.11707	
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	1	237.292	212.457	1.11689	
252	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	0	10551.6	11573.5	1.09685	
253	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	0	10551.6	11573.5	1.09685	
253	mad protein (max dimerizer). [source:swissprot;acc:q05195]	1	228	204.333	1.11583	
254	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	0	10551.6	11573.5	1.09685	
254	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	1	200.691	179.88	1.11569	
255	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	1	200.691	179.88	1.11569	
255	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	0	10551.6	11573.5	1.09685	
256	espin. [source:refseq;acc:nm_031475]	0	10551.6	11573.4	1.09684	
256	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	1	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]	1	200.691	179.88	1.11569	
257	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	0	10552.2	11566.4	1.09611	
258	40s ribosomal protein s28. [source:swissprot;acc:p25112]	0	12967.1	14193.6	1.09459	
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	1	227.999	204.366	1.11564	
259	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	0	10438.3	9549.77	1.09304	
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	1	227.999	204.37	1.11562	
260	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	0	12447.6	11392.6	1.0926	
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	1	219.421	196.978	1.11394	
261	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	0	12448.9	11393.9	1.09259	
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	1	219.421	196.978	1.11394	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	1	219.421	196.978	1.11394	
262	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	0	3464	3778	1.09065	
263	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	0	13573.3	14801.2	1.09046	
263	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	1	219.421	196.978	1.11394	
264	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	0	10037.1	10935.1	1.08947	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	1	219.421	196.978	1.11394	
265	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [source:swissprot;acc:o15488]	0	13653.8	14874	1.08937	
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]	1	225.217	202.459	1.11241	
266	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	0	13483.3	14685.4	1.08915	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	1	241.07	267.88	1.11121	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	1	241.07	267.88	1.11121	
267	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [source:swissprot;acc:o00268]	0	8054.34	8772.02	1.0891	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	1	271.016	244.167	1.10996	
268	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [source:swissprot;acc:q14168]	0	14257.4	13134.5	1.08549	
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]	1	241.373	267.352	1.10763	
269	ischemia/reperfusion inducible protein. [source:refseq;acc:nm_024640]	0	12463.5	11482.6	1.08542	
270	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	0	10735.1	9891.37	1.0853	
270	fad synthetase. [source:refseq;acc:nm_025207]	1	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]	1	241.373	267.352	1.10763	
271	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	0	10735.1	9891.37	1.0853	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	1	241.373	267.352	1.10763	
272	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	0	7163.55	7759.61	1.08321	
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]	1	241.373	267.352	1.10763	
273	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	0	12748.1	11770.9	1.08302	

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/