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 Gene Network Comparison Type description Interaction Map red green Filtered network_comparison

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Showing element 1 to 50 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	Network Comparison Type	description	red	green	Filtered	network_comparison
1	Measured	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	0	36400000
		Divided	rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	2394.5	1	5.31521
		Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	6410	0	6325
		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]	41482.5	33356.5	1	8126
	Ranked	Divided	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	15915	0	3.70633
		Divided	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	24	1	2.4
		Subtracted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	322	1	107
		Subtracted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	21883	0	12977
	Squared	Divided	cab2. [refseq;acc:nm_033419]	0.00001	7.16592	0	716592
		Divided	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.0356	1357.07	1	28.2513
		Subtracted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	232467	160184	0	72283
		Subtracted	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	468498	322755	1	145743
	Rooted	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	0.00001	0	1907880
		Divided	rad50-interacting protein 1. [refseq;acc:nm_021930]	21.225	48.9336	1	2.30547
		Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	9.20014	60.0707	0	50.8706
		Subtracted	rad50-interacting protein 1. [refseq;acc:nm_021930]	21.225	48.9336	1	27.7086
2	Measured	Divided	cab2. [refseq;acc:nm_033419]	0.00001	174	0	17400000
		Divided	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	2394.5	1	5.31521
		Subtracted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	41482.5	33356.5	1	8126
		Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	85	6410	0	6325
	Ranked	Divided	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]	15	28	1	1.86667
		Divided	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	14977	0	2.55362
		Subtracted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	15915	0	11621
		Subtracted	hbs1-like. [refseq;acc:nm_006620]	215	322	1	107
	Squared	Divided	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325	0.00001	0	561325
		Divided	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.0356	1357.07	1	28.2513
		Subtracted	histone h4. [swissprot;acc:p02304]	273623	345123	0	71500
		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]	407289	263351	1	143938
	Rooted	Divided	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	12.4097	0.00001	0	1240970
		Divided	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	21.225	48.9336	1	2.30547
		Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	9.20014	60.0707	0	50.8706
		Subtracted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	21.225	48.9336	1	27.7086
3	Measured	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	698.5	1	3.71868
		Divided	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	109	0	10900000
		Subtracted	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	41482.5	33356.5	1	8126
		Subtracted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	23818.1	19621.3	0	4196.8
	Ranked	Divided	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15	28	1	1.86667
		Divided	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84	11083.9	0	2.47638
		Subtracted	cab2. [refseq;acc:nm_033419]	21866	10950	0	10916
		Subtracted	rad50-interacting protein 1. [refseq;acc:nm_021930]	337	232	1	105
	Squared	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1596.92	115.48	1	13.8285
		Divided	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	5.61325	0.00001	0	561325
		Subtracted	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	135280	170628	0	35348
		Subtracted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	407289	263351	1	143938
	Rooted	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	50.9657	26.4292	1	1.92839
		Divided	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	12.4097	0.00001	0	1240970
		Subtracted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	36.9188	6.85565	0	30.0631
		Subtracted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	50.9657	26.4292	1	24.5365
4	Measured	Divided	hbs1-like. [refseq;acc:nm_006620]	2597.5	698.5	1	3.71868
4	Measured	Divided	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	89	0	8900000

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/