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

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Showing element 1 to 50 of 19268 in total

Value Type

: Measured

Rank	red	Network Comparison Type	description	Filtered	Interaction Map	green	network_comparison
1	85	Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	High confidence	6410	6325
	85	Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Low confidence	6410	6325
	364	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		High confidence	0.00001	36400000
	364				Low confidence	0.00001	36400000
	450.5		rad50-interacting protein 1. [refseq;acc:nm_021930]	1	High confidence	2394.5	5.31521
	2399.5		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Low confidence	543.5	4.4149
	40899	Subtracted	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		Low confidence	32028.5	8870.5
	41482.5	Subtracted	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]		High confidence	33356.5	8126
2	0.00001	Divided	cab2. [refseq;acc:nm_033419]	0	High confidence	174	17400000
	0.00001	Divided	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Low confidence	89	8900000
	85	Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		High confidence	6410	6325
	450.5	Divided	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	High confidence	2394.5	5.31521
	2399.5	Divided	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		Low confidence	543.5	4.4149
	21185	Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]			28492	7307
	23818.1		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0		19621.3	4196.8
	41482.5		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	High confidence	33356.5	8126
3	0.00001	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	Low confidence	89	8900000
	0.00001		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	High confidence	109	10900000
	2399.5		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	Low confidence	543.5	4.4149
	2597.5		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	High confidence	698.5	3.71868
	5106.93	Subtracted	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	0	Low confidence	7500.75	2393.82
	21185		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	1	Low confidence	28492	7307
	23818.1		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	High confidence	19621.3	4196.8
	41482.5		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	High confidence	33356.5	8126
4	0.00001	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	Low confidence	89	8900000
	0.00001	Divided	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		High confidence	89	8900000
	2082	Subtracted	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]		Low confidence	4356	2274
	2399.5	Divided	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1	Low confidence	543.5	4.4149
	2597.5	Divided	hbs1-like. [refseq;acc:nm_006620]	1	High confidence	698.5	3.71868
	18704	Subtracted	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	0	High confidence	21730	3026
	36474.3		bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	1	Low confidence	43509.4	7035.1
	41482.5		cytohesin 4. [swissprot;acc:q9uia0]	1	High confidence	33356.5	8126
5	0.00001	Divided	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	High confidence	89	8900000
	0.00001	Divided	jumonji protein. [swissprot;acc:q92833]		Low confidence	17.5166	1751660
	485.286	Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]			2740.13	2254.84
	736.5	Divided	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1		2113.5	2.86965
	1153.5	Divided	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1	High confidence	339.5	3.39764
	21773.1	Subtracted	histone h4. [swissprot;acc:p02304]	0	High confidence	24446.3	2673.2
	36469.3		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	1	Low confidence	43503.3	7034
	41482.5		cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	1	High confidence	33356.5	8126
6	0.00001	Divided	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	High confidence	89	8900000
	13		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0	Low confidence	0.00001	1300000
	736.5		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	1	Low confidence	2113.5	2.86965
	1153.5		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1	High confidence	339.5	3.39764
	7592.37	Subtracted	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	0	Low confidence	8836.85	1244.48
	13174.7		similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	0	High confidence	15605.1	2430.4
	36360.3		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	1	Low confidence	43368.8	7008.5
	44490.5		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	High confidence	36927.5	7563
7	0.00001	Divided	sedlin. [swissprot;acc:o14582]	0	High confidence	43	4300000
7	2.31962	Divided	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	0	Low confidence	0.00001	231962

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/