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 1025 to 1074 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
257	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Rooted	51.6125	45.8409	1.12591	
257	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Measured	6417.31	7858.12	1.22452	
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	200.691	179.88	1.11569	
257	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Squared	15482.3	20162.4	1.30229	
258	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Measured	6417.33	7857.93	1.22449	
258	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	Squared	76438	58889.7	1.29799	
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Ranked	227.999	204.366	1.11564	
258	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Rooted	51.6132	45.8422	1.12589	
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	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	227.999	204.37	1.11562	
259	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Measured	6417.81	7852.52	1.22355	
259	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Rooted	58.2964	65.5926	1.12516	
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Ranked	219.421	196.978	1.11394	
260	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	Squared	76296.4	58801.6	1.29752	
260	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Rooted	59.0951	66.4332	1.12417	
260	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Measured	4244.95	5193.42	1.22343	
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Ranked	219.421	196.978	1.11394	
261	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	Squared	48127.9	62245.6	1.29334	
261	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Rooted	62.3337	70.0738	1.12417	
261	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Measured	4247.36	5192.61	1.22255	
262	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	Measured	24896.4	20431.7	1.21852	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Ranked	219.421	196.978	1.11394	
262	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Squared	26157.6	20236.2	1.29261	
262	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Rooted	59.4073	66.7002	1.12276	
263	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Squared	26157.6	20236.2	1.29261	
263	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Ranked	219.421	196.978	1.11394	
263	paxillin. [source:swissprot;acc:p49023]	Rooted	59.4073	66.7002	1.12276	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	Measured	24896.4	20431.7	1.21852	
264	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Squared	26157.6	20236.2	1.29261	
264	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Measured	4987.58	4094.57	1.2181	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Ranked	219.421	196.978	1.11394	
264	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Rooted	66.1122	74.1438	1.12148	
265	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Squared	26157.6	20236.2	1.29261	
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]	Ranked	225.217	202.459	1.11241	
265	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Rooted	56.031	62.8281	1.12131	
265	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Measured	24806.9	20369.9	1.21782	
266	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Measured	24806.9	20369.9	1.21782	
266	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Squared	26157.6	20236.2	1.29261	
266	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Rooted	66.1064	74.1074	1.12103	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Ranked	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]	Ranked	241.07	267.88	1.11121	
267	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Squared	26157.6	20236.2	1.29261	
267	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Measured	14021.4	11523	1.21682	
267	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Rooted	66.1064	74.1073	1.12103	
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Measured	24473.9	20127.8	1.21593	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Ranked	271.016	244.167	1.10996	
268	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Squared	26157.6	20236.2	1.29261	
268	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Rooted	66.1064	74.1074	1.12103	
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]	Ranked	241.373	267.352	1.10763	
269	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Squared	26157.6	20236.2	1.29261	

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/