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 51 to 100 of 33156 in total

Network Comparison Type	Divided
Filtered	1

Rank	description	Value Type	Interaction Map	red	green	network_comparison	
7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Measured	Low confidence	736.5	2113.5	2.86965	
7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Squared	Low confidence	128.386	1057.25	8.23493	
7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Rooted	Low confidence	27.1385	45.9728	1.69401	
7	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Measured	High confidence	1153.5	339.5	3.39764	
7	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Squared	High confidence	314.926	27.2805	11.544	
7	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Rooted	High confidence	33.9632	18.4255	1.84327	
8	db83 protein. [source:swissprot;acc:p57088]	Measured	High confidence	1153.5	339.5	3.39764	
8	db83 protein. [source:swissprot;acc:p57088]	Squared	High confidence	314.926	27.2805	11.544	
8	db83 protein. [source:swissprot;acc:p57088]	Rooted	High confidence	33.9632	18.4255	1.84327	
8	hbs1-like. [source:refseq;acc:nm_006620]	Ranked	High confidence	215	322	1.49767	
8	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Ranked	Low confidence	318	240	1.325	
8	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [source:swissprot;acc:q07326]	Measured	Low confidence	3278	5058.5	1.54317	
8	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [source:swissprot;acc:q07326]	Squared	Low confidence	2543.26	6056.43	2.38136	
8	thyroid receptor interacting protein 8 (trip-8) (fragment). [source:swissprot;acc:q15652]	Rooted	Low confidence	31.8641	47.6922	1.49674	
9	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Ranked	Low confidence	58	44	1.31818	
9	gbp protein isoform a. [source:refseq;acc:nm_017870]	Rooted	Low confidence	31.8923	47.7107	1.49599	
9	n33 protein. [source:swissprot;acc:q13454]	Measured	Low confidence	3278	5058.5	1.54317	
9	n33 protein. [source:swissprot;acc:q13454]	Squared	Low confidence	2543.26	6056.43	2.38136	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Measured	High confidence	398.5	1281.5	3.21581	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Squared	High confidence	37.5863	388.696	10.3414	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Rooted	High confidence	19.9625	35.798	1.79326	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Ranked	High confidence	212	309	1.45755	
10	implantation-associated protein. [source:refseq;acc:nm_032121]	Measured	Low confidence	3278	5058.5	1.54317	
10	implantation-associated protein. [source:refseq;acc:nm_032121]	Squared	Low confidence	2543.26	6056.43	2.38136	
10	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [source:refseq;acc:nm_018433]	Rooted	Low confidence	31.9296	47.7352	1.49501	
10	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Ranked	Low confidence	58	44	1.31818	
10	protein x 0004. [source:refseq;acc:nm_016301]	Ranked	High confidence	212	309	1.45755	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Measured	High confidence	398.5	1281.5	3.21581	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Squared	High confidence	37.5863	388.696	10.3414	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Rooted	High confidence	19.9625	35.798	1.79326	
11	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Squared	Low confidence	106226	192141	1.80879	
11	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Ranked	Low confidence	37.318	28.4944	1.30966	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Measured	High confidence	398.5	1281.5	3.21581	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Squared	High confidence	37.5863	388.696	10.3414	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Rooted	High confidence	19.9625	35.798	1.79326	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Ranked	High confidence	337	232	1.45259	
11	thyroid receptor interacting protein 8 (trip-8) (fragment). [source:swissprot;acc:q15652]	Measured	Low confidence	1917.64	2950.5	1.53861	
11	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [source:swissprot;acc:p35030]	Rooted	Low confidence	32.2231	47.928	1.48738	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Measured	High confidence	398.5	1281.5	3.21581	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Squared	High confidence	37.5863	388.696	10.3414	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Rooted	High confidence	19.9625	35.798	1.79326	
12	gbp protein isoform a. [source:refseq;acc:nm_017870]	Measured	Low confidence	1921.96	2954.24	1.5371	
12	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Squared	Low confidence	106226	192141	1.80879	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Ranked	High confidence	337	232	1.45259	
12	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [source:swissprot;acc:p07477]	Rooted	Low confidence	32.2966	47.9763	1.48549	
12	vitelliform macular dystrophy 2-like protein 2. [source:refseq;acc:nm_153274]	Ranked	Low confidence	37.3475	28.5242	1.30933	
13	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	Rooted	Low confidence	39.2301	52.5277	1.33896	
13	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Squared	Low confidence	395912	242799	1.63062	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Measured	High confidence	398.5	1281.5	3.21581	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Squared	High confidence	37.5863	388.696	10.3414	

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/