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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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Value Type Rank Gene description Interaction Map Network Comparison Type red Filtered green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 66312 in total

Value Type	Measured
Filtered	1

Rank	description	Interaction Map	Network Comparison Type	red	green	network_comparison	
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	Subtracted	40899	32028.5	8870.5	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	Divided	2399.5	543.5	4.4149	
1	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	High confidence	Subtracted	41482.5	33356.5	8126	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	Divided	450.5	2394.5	5.31521	
2	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Low confidence	Subtracted	21185	28492	7307	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	Divided	2399.5	543.5	4.4149	
2	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	High confidence	Subtracted	41482.5	33356.5	8126	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	Divided	450.5	2394.5	5.31521	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	Divided	2399.5	543.5	4.4149	
3	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	High confidence	Subtracted	41482.5	33356.5	8126	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	Divided	2597.5	698.5	3.71868	
3	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Low confidence	Subtracted	21185	28492	7307	
4	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Low confidence	Subtracted	36474.3	43509.4	7035.1	
4	cytohesin 4. [source:swissprot;acc:q9uia0]	High confidence	Subtracted	41482.5	33356.5	8126	
4	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	Divided	2597.5	698.5	3.71868	
4	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	Divided	2399.5	543.5	4.4149	
5	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	High confidence	Subtracted	41482.5	33356.5	8126	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	Divided	1153.5	339.5	3.39764	
5	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	Divided	736.5	2113.5	2.86965	
5	vitelliform macular dystrophy 2-like protein 2. [source:refseq;acc:nm_153274]	Low confidence	Subtracted	36469.3	43503.3	7034	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	Divided	1153.5	339.5	3.39764	
6	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Low confidence	Subtracted	36360.3	43368.8	7008.5	
6	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	Divided	736.5	2113.5	2.86965	
6	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	High confidence	Subtracted	44490.5	36927.5	7563	
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	High confidence	Subtracted	21185	28492	7307	
7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Low confidence	Divided	736.5	2113.5	2.86965	
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]	High confidence	Divided	1153.5	339.5	3.39764	
7	vitelliform macular dystrophy 2-like protein 1. [source:refseq;acc:nm_017682]	Low confidence	Subtracted	36360.3	43368.8	7008.5	
8	db83 protein. [source:swissprot;acc:p57088]	High confidence	Divided	1153.5	339.5	3.39764	
8	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Low confidence	Subtracted	33111.4	39358.1	6246.7	
8	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	High confidence	Subtracted	21185	28492	7307	
8	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [source:swissprot;acc:q07326]	Low confidence	Divided	3278	5058.5	1.54317	
9	n33 protein. [source:swissprot;acc:q13454]	Low confidence	Divided	3278	5058.5	1.54317	
9	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	High confidence	Subtracted	21185	28492	7307	
9	sperm associated antigen 7. [source:refseq;acc:nm_004890]	Low confidence	Subtracted	23318	19280.8	4037.2	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	High confidence	Divided	398.5	1281.5	3.21581	
10	implantation-associated protein. [source:refseq;acc:nm_032121]	Low confidence	Divided	3278	5058.5	1.54317	
10	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	High confidence	Subtracted	21185	28492	7307	
10	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Low confidence	Subtracted	19498.1	17265.4	2232.7	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	High confidence	Divided	398.5	1281.5	3.21581	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	High confidence	Divided	398.5	1281.5	3.21581	
11	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	High confidence	Subtracted	21185	28492	7307	
11	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Low confidence	Subtracted	7256.71	9368.87	2112.16	
11	thyroid receptor interacting protein 8 (trip-8) (fragment). [source:swissprot;acc:q15652]	Low confidence	Divided	1917.64	2950.5	1.53861	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	High confidence	Divided	398.5	1281.5	3.21581	
12	gbp protein isoform a. [source:refseq;acc:nm_017870]	Low confidence	Divided	1921.96	2954.24	1.5371	
12	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Low confidence	Subtracted	15464.1	17572.7	2108.6	
12	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	High confidence	Subtracted	34190.9	40795.8	6604.9	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	High confidence	Divided	398.5	1281.5	3.21581	
13	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Low confidence	Subtracted	15464.1	17572.7	2108.6	

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/