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.


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Rank Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
251	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Rooted	0	21.3142	23.5833	1.10646	
251	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	Squared	1	69165.6	52992.1	1.30521	
251	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	Ranked	0	10551.6	11573.6	1.09686	
251	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	Measured	0	1225.08	1079.38	1.13498	
251	max protein. [source:swissprot;acc:p25912]	Rooted	1	56.3054	63.7148	1.13159	
251	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Ranked	1	186.172	166.661	1.11707	
251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Measured	1	6417.18	7859.6	1.22477	
251	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [source:swissprot;acc:q9upy6]	Squared	0	25574.2	20063.8	1.27464	
252	crk-like protein. [source:swissprot;acc:p46109]	Measured	1	6417.18	7859.6	1.22477	
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Ranked	1	237.292	212.457	1.11689	
252	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	Ranked	0	10551.6	11573.5	1.09685	
252	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [source:swissprot;acc:p36776]	Rooted	0	21.1331	19.1063	1.10608	
252	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]	Rooted	1	51.6736	58.4422	1.13099	
252	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	Squared	1	69165	52991.7	1.3052	
252	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]	Squared	0	803.941	631.169	1.27373	
252	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	Measured	0	1225.08	1079.38	1.13498	
253	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	Squared	1	69165	52991.7	1.3052	
253	espin. [source:refseq;acc:nm_031475]	Measured	0	1225.07	1079.38	1.13498	
253	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	Ranked	0	10551.6	11573.5	1.09685	
253	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Ranked	1	228	204.333	1.11583	
253	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Squared	0	46977	36903.3	1.27298	
253	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Measured	1	6417.18	7859.59	1.22477	
253	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [source:swissprot;acc:p15154]	Rooted	0	8.05424	8.90701	1.10588	
253	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Rooted	1	53.5956	60.465	1.12817	
254	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Measured	0	1318.22	1495.66	1.13461	
254	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	Squared	0	220.878	173.801	1.27087	
254	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	Ranked	0	10551.6	11573.5	1.09685	
254	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Measured	1	6417.18	7859.6	1.22477	
254	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [source:swissprot;acc:o14658]	Rooted	0	8.05424	8.90701	1.10588	
254	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Rooted	1	53.607	60.4452	1.12756	
254	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Ranked	1	200.691	179.88	1.11569	
254	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	Squared	1	69165	52991.7	1.3052	
255	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Measured	0	1317.84	1495.22	1.1346	
255	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	Squared	1	69123.3	52967	1.30503	
255	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	Rooted	0	28.4183	31.4149	1.10545	
255	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	Squared	0	220.837	280.438	1.26989	
255	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Ranked	1	200.691	179.88	1.11569	
255	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Measured	1	6417.18	7859.6	1.22477	
255	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Rooted	1	62.9007	70.8854	1.12694	
255	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	Ranked	0	10551.6	11573.5	1.09685	
256	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	Rooted	1	48.0045	54.0843	1.12665	
256	espin. [source:refseq;acc:nm_031475]	Ranked	0	10551.6	11573.4	1.09684	
256	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Squared	1	15465.1	20151	1.303	
256	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	Squared	0	4766.78	3763.9	1.26645	
256	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	Rooted	0	24.8155	27.4116	1.10462	
256	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	Measured	1	6417.19	7859.51	1.22476	
256	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	Measured	0	1224.65	1079.77	1.13418	
256	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Ranked	1	227.999	204.357	1.11569	
257	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Rooted	0	21.1374	23.3445	1.10442	
257	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Rooted	1	51.6125	45.8409	1.12591	

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/