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 2030 to 2079 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
254	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
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Rooted	1	51.6125	45.8409	1.12591
	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	Measured	1	6417.31	7858.12	1.22452
	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Measured	0	861.401	759.896	1.13358
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Ranked	1	200.691	179.88	1.11569
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared	1	15482.3	20162.4	1.30229
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Ranked	0	10552.2	11566.4	1.09611
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Squared		1.60583	1.26833	1.2661
258	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Measured		1183.16	1337.54	1.13048
	40s ribosomal protein s28. [swissprot;acc:p25112]	Ranked		12967.1	14193.6	1.09459
	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Rooted		21.1334	23.34	1.10441
	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Squared		2783.53	3517.26	1.2636
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Measured	1	6417.33	7857.93	1.22449
	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	Squared		76438	58889.7	1.29799
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Ranked		227.999	204.366	1.11564
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Rooted		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). [swissprot;acc:p08865]	Rooted	0	21.9471	19.8816	1.10389
	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Squared		3438.01	4339.96	1.26235
	60s ribosomal protein l23a. [swissprot;acc:p29316]	Measured		1295.49	1463.51	1.1297
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Ranked		10438.3	9549.77	1.09304
	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). [swissprot;acc:q9y5p4]	Squared	1	76360.8	58841.7	1.29773
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Ranked		227.999	204.37	1.11562
	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	Measured		6417.81	7852.52	1.22355
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Rooted		58.2964	65.5926	1.12516
260	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Ranked	0	12447.6	11392.6	1.0926
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Ranked	1	219.421	196.978	1.11394
	histone h4. [swissprot;acc:p02304]	Squared	0	273623	345123	1.26131
	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	Squared	1	76296.4	58801.6	1.29752
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Rooted	1	59.0951	66.4332	1.12417
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Rooted	0	22.3157	24.6207	1.10329
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Measured	1	4244.95	5193.42	1.22343

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/