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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2025 to 2074 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
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	
257	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Measured	1	6417.31	7858.12	1.22452	
257	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	Measured	0	861.401	759.896	1.13358	
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]	Ranked	1	200.691	179.88	1.11569	
257	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Squared	1	15482.3	20162.4	1.30229	
257	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	Ranked	0	10552.2	11566.4	1.09611	
257	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	Squared	0	1.60583	1.26833	1.2661	
258	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Measured	0	1183.16	1337.54	1.13048	
258	40s ribosomal protein s28. [source:swissprot;acc:p25112]	Ranked	0	12967.1	14193.6	1.09459	
258	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Rooted	0	21.1334	23.34	1.10441	
258	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	Squared	0	2783.53	3517.26	1.2636	
258	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Measured	1	6417.33	7857.93	1.22449	
258	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	Squared	1	76438	58889.7	1.29799	
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Ranked	1	227.999	204.366	1.11564	
258	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Rooted	1	51.6132	45.8422	1.12589	
259	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Rooted	0	21.9471	19.8816	1.10389	
259	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Squared	0	3438.01	4339.96	1.26235	
259	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Measured	0	1295.49	1463.51	1.1297	
259	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	Ranked	0	10438.3	9549.77	1.09304	
259	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4]	Squared	1	76360.8	58841.7	1.29773	
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Ranked	1	227.999	204.37	1.11562	
259	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Measured	1	6417.81	7852.52	1.22355	
259	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Rooted	1	58.2964	65.5926	1.12516	
260	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Ranked	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]	Ranked	1	219.421	196.978	1.11394	

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/