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

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Showing element 1 to 50 of 77072 in total

Value Type

: Measured

Rank	Filtered	description	Network Comparison Type	Interaction Map	green	network_comparison	red
1	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	High confidence	6410	6325	85
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	Low confidence	6410	6325	85
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	High confidence	0.00001	36400000	364
			Divided	Low confidence	0.00001	36400000	364
	1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Subtracted		32028.5	8870.5	40899
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided		543.5	4.4149	2399.5
		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]	Subtracted	High confidence	33356.5	8126	41482.5
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Divided		2394.5	5.31521	450.5
2	0	cab2. [refseq;acc:nm_033419]			174	17400000	0.00001
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	89	8900000	0.00001
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	High confidence	6410	6325	85
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Low confidence	19621.3	4196.8	23818.1
	1	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]			28492	7307	21185
		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided		543.5	4.4149	2399.5
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Subtracted	High confidence	33356.5	8126	41482.5
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	High confidence	2394.5	5.31521	450.5
3	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	Low confidence	89	8900000	0.00001
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	High confidence	19621.3	4196.8	23818.1
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	Low confidence	7500.75	2393.82	5106.93
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	High confidence	109	10900000	0.00001
	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Divided	Low confidence	543.5	4.4149	2399.5
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Subtracted	High confidence	33356.5	8126	41482.5
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	High confidence	698.5	3.71868	2597.5
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	Low confidence	28492	7307	21185
4	0	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Subtracted		4356	2274	2082
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided		89	8900000	0.00001
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	High confidence	89	8900000	0.00001
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	High confidence	21730	3026	18704
	1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]		Low confidence	43509.4	7035.1	36474.3
		cytohesin 4. [swissprot;acc:q9uia0]		High confidence	33356.5	8126	41482.5
		hbs1-like. [refseq;acc:nm_006620]	Divided	High confidence	698.5	3.71868	2597.5
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Divided	Low confidence	543.5	4.4149	2399.5
5	0	histone h4. [swissprot;acc:p02304]	Subtracted	High confidence	24446.3	2673.2	21773.1
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	High confidence	89	8900000	0.00001
		jumonji protein. [swissprot;acc:q92833]	Divided	Low confidence	17.5166	1751660	0.00001
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	Low confidence	2740.13	2254.84	485.286
	1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Subtracted	High confidence	33356.5	8126	41482.5
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	High confidence	339.5	3.39764	1153.5
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Divided	Low confidence	2113.5	2.86965	736.5
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Subtracted	Low confidence	43503.3	7034	36469.3
6	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	High confidence	89	8900000	0.00001
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Divided	Low confidence	0.00001	1300000	13
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	High confidence	15605.1	2430.4	13174.7
		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	Low confidence	8836.85	1244.48	7592.37
	1	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	High confidence	339.5	3.39764	1153.5
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	Low confidence	43368.8	7008.5	36360.3
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Divided	Low confidence	2113.5	2.86965	736.5
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Subtracted	High confidence	36927.5	7563	44490.5
7	0	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Subtracted	Low confidence	5898.71	1238.62	4660.09
7	0	sedlin. [swissprot;acc:o14582]	Divided	High confidence	43	4300000	0.00001

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/