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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Network Comparison Type

: Divided

Rank	Interaction Map	Value Type	green	description	Filtered	network_comparison	red
1	High confidence	Measured	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	36400000	364
		Measured	2394.5	rad50-interacting protein 1. [refseq;acc:nm_021930]	1	5.31521	450.5
		Ranked	24	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	2.4	10
		Ranked	15915	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	3.70633	4294
		Squared	7.16592	cab2. [refseq;acc:nm_033419]	0	716592	0.00001
		Squared	1357.07	rad50-interacting protein 1. [refseq;acc:nm_021930]	1	28.2513	48.0356
		Rooted	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	1907880	19.0788
		Rooted	48.9336	rad50-interacting protein 1. [refseq;acc:nm_021930]	1	2.30547	21.225
	Low confidence	Measured	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	36400000	364
		Measured	543.5	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	4.4149	2399.5
		Ranked	32	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1	2	16
		Ranked	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	2.55362	5865
		Squared	1.87479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	187479	0.00001
		Squared	69.9153	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	19.4914	1362.75
		Rooted	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	1907880	19.0788
		Rooted	23.3131	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	2.10117	48.9847
2	High confidence	Measured	174	cab2. [refseq;acc:nm_033419]	0	17400000	0.00001
		Measured	2394.5	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	5.31521	450.5
		Ranked	28	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). [swissprot;acc:o60476]	1	1.86667	15
		Ranked	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	2.55362	5865
		Squared	0.00001	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0	561325	5.61325
		Squared	1357.07	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	28.2513	48.0356
		Rooted	0.00001	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0	1240970	12.4097
		Rooted	48.9336	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	2.30547	21.225
	Low confidence	Measured	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	8900000	0.00001
		Measured	543.5	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	4.4149	2399.5
		Ranked	330	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	1.47982	223
		Ranked	21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	2.45711	8906
		Squared	1.87479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	187479	0.00001
		Squared	69.9153	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	19.4914	1362.75
		Rooted	9.43398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	943398	0.00001
		Rooted	23.3131	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	2.10117	48.9847
3	High confidence	Measured	109	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	10900000	0.00001
		Measured	698.5	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	3.71868	2597.5
		Ranked	28	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	1.86667	15
		Ranked	11083.9	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	2.47638	4475.84
		Squared	0.00001	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	561325	5.61325
		Squared	115.48	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	13.8285	1596.92
		Rooted	0.00001	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	1240970	12.4097
		Rooted	26.4292	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	1.92839	50.9657
	Low confidence	Measured	89	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	8900000	0.00001
		Measured	543.5	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	4.4149	2399.5
		Ranked	330	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	1.47982	223
		Ranked	20617	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	0	2.14604	9607
		Squared	1.87479	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	187479	0.00001
		Squared	69.9153	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	19.4914	1362.75
		Rooted	9.43398	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	943398	0.00001
		Rooted	23.3131	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	2.10117	48.9847
4	High confidence	Measured	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	8900000	0.00001
4	High confidence	Measured	698.5	hbs1-like. [refseq;acc:nm_006620]	1	3.71868	2597.5

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/