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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Network Comparison Type	Divided

Rank	Value Type	Filtered	description	Interaction Map	red	green	network_comparison	
1	Measured	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	High confidence	364	0.00001	36400000	
1	Measured	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Low confidence	364	0.00001	36400000	
1	Measured	1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	2399.5	543.5	4.4149	
1	Measured	1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	450.5	2394.5	5.31521	
1	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	High confidence	4294	15915	3.70633	
1	Ranked	0	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Low confidence	5865	14977	2.55362	
1	Ranked	1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	16	32	2	
1	Ranked	1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	High confidence	10	24	2.4	
1	Squared	0	cab2. [source:refseq;acc:nm_033419]	High confidence	0.00001	7.16592	716592	
1	Squared	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Low confidence	0.00001	1.87479	187479	
1	Squared	1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	1362.75	69.9153	19.4914	
1	Squared	1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	48.0356	1357.07	28.2513	
1	Rooted	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	High confidence	19.0788	0.00001	1907880	
1	Rooted	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Low confidence	19.0788	0.00001	1907880	
1	Rooted	1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	48.9847	23.3131	2.10117	
1	Rooted	1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	21.225	48.9336	2.30547	
2	Measured	0	cab2. [source:refseq;acc:nm_033419]	High confidence	0.00001	174	17400000	
2	Measured	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Low confidence	0.00001	89	8900000	
2	Measured	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	2399.5	543.5	4.4149	
2	Measured	1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	450.5	2394.5	5.31521	
2	Ranked	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Low confidence	8906	21883	2.45711	
2	Ranked	0	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	High confidence	5865	14977	2.55362	
2	Ranked	1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	223	330	1.47982	
2	Ranked	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	15	28	1.86667	
2	Squared	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Low confidence	0.00001	1.87479	187479	
2	Squared	0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	High confidence	5.61325	0.00001	561325	
2	Squared	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	1362.75	69.9153	19.4914	
2	Squared	1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	48.0356	1357.07	28.2513	
2	Rooted	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Low confidence	0.00001	9.43398	943398	
2	Rooted	0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	High confidence	12.4097	0.00001	1240970	
2	Rooted	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	48.9847	23.3131	2.10117	
2	Rooted	1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	21.225	48.9336	2.30547	
3	Measured	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Low confidence	0.00001	89	8900000	
3	Measured	0	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	High confidence	0.00001	109	10900000	
3	Measured	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	2399.5	543.5	4.4149	
3	Measured	1	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	2597.5	698.5	3.71868	
3	Ranked	0	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [source:swissprot;acc:p46531]	Low confidence	9607	20617	2.14604	
3	Ranked	0	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	High confidence	4475.84	11083.9	2.47638	
3	Ranked	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	223	330	1.47982	
3	Ranked	1	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	High confidence	15	28	1.86667	
3	Squared	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Low confidence	0.00001	1.87479	187479	
3	Squared	0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	High confidence	5.61325	0.00001	561325	
3	Squared	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	1362.75	69.9153	19.4914	
3	Squared	1	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	1596.92	115.48	13.8285	
3	Rooted	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Low confidence	0.00001	9.43398	943398	
3	Rooted	0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	High confidence	12.4097	0.00001	1240970	
3	Rooted	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	48.9847	23.3131	2.10117	
3	Rooted	1	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	50.9657	26.4292	1.92839	
4	Measured	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Low confidence	0.00001	89	8900000	
4	Measured	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	High confidence	0.00001	89	8900000	

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/