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 2001 to 2050 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
251	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Rooted	0	21.3142	23.5833	1.10646
	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	Squared	1	69165.6	52992.1	1.30521
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Ranked	0	10551.6	11573.6	1.09686
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Measured	0	1225.08	1079.38	1.13498
	max protein. [swissprot;acc:p25912]	Rooted	1	56.3054	63.7148	1.13159
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Ranked		186.172	166.661	1.11707
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	Measured		6417.18	7859.6	1.22477
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Squared	0	25574.2	20063.8	1.27464
252	crk-like protein. [swissprot;acc:p46109]	Measured	1	6417.18	7859.6	1.22477
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Ranked	1	237.292	212.457	1.11689
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Ranked	0	10551.6	11573.5	1.09685
	lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776]	Rooted	0	21.1331	19.1063	1.10608
	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). [swissprot;acc:p25208]	Rooted	1	51.6736	58.4422	1.13099
	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	Squared	1	69165	52991.7	1.3052
	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). [refseq;acc:nm_016538]	Squared	0	803.941	631.169	1.27373
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [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). [swissprot;acc:p41182]	Squared	1	69165	52991.7	1.3052
	espin. [refseq;acc:nm_031475]	Measured	0	1225.07	1079.38	1.13498
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Ranked	0	10551.6	11573.5	1.09685
	mad protein (max dimerizer). [swissprot;acc:q05195]	Ranked	1	228	204.333	1.11583
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Squared	0	46977	36903.3	1.27298
	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]	Measured	1	6417.18	7859.59	1.22477
	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	Rooted	0	8.05424	8.90701	1.10588
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Rooted	1	53.5956	60.465	1.12817
254	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Measured	0	1318.22	1495.66	1.13461
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Squared		220.878	173.801	1.27087
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Ranked		10551.6	11573.5	1.09685
	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	Measured	1	6417.18	7859.6	1.22477
	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	Rooted	0	8.05424	8.90701	1.10588
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Rooted	1	53.607	60.4452	1.12756
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Ranked		200.691	179.88	1.11569
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Squared		69165	52991.7	1.3052
255	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Measured	0	1317.84	1495.22	1.1346
	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	Squared	1	69123.3	52967	1.30503
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	Rooted	0	28.4183	31.4149	1.10545
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Squared	0	220.837	280.438	1.26989
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Ranked	1	200.691	179.88	1.11569
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Measured		6417.18	7859.6	1.22477
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Rooted		62.9007	70.8854	1.12694
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Ranked	0	10551.6	11573.5	1.09685
256	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Rooted	1	48.0045	54.0843	1.12665
	espin. [refseq;acc:nm_031475]	Ranked	0	10551.6	11573.4	1.09684
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Squared	1	15465.1	20151	1.303
	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Squared	0	4766.78	3763.9	1.26645
	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	Rooted	0	24.8155	27.4116	1.10462
	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). [swissprot;acc:o75791]	Measured	1	6417.19	7859.51	1.22476
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Measured	0	1224.65	1079.77	1.13418
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Ranked	1	227.999	204.357	1.11569
257	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Rooted	0	21.1374	23.3445	1.10442
257	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Rooted	1	51.6125	45.8409	1.12591

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/