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 description green Gene Interaction Map Network Comparison Type network_comparison red

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	Filtered	description	green	Network Comparison Type	network_comparison	red
1	Measured	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	Subtracted	6325	85
		0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Divided	36400000	364
		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). [swissprot;acc:o60476]	33356.5	Subtracted	8126	41482.5
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5	Divided	5.31521	450.5
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	Divided	3.70633	4294
		0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	Subtracted	12977	8906
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	Subtracted	107	215
		1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	Divided	2.4	10
	Squared	0	cab2. [refseq;acc:nm_033419]	7.16592	Divided	716592	0.00001
		0	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	Subtracted	72283	232467
		1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	322755	Subtracted	145743	468498
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	Divided	28.2513	48.0356
	Rooted	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	Subtracted	50.8706	9.20014
		0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	Divided	1907880	19.0788
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	Divided	2.30547	21.225
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	Subtracted	27.7086	21.225
2	Measured	0	cab2. [refseq;acc:nm_033419]	174	Divided	17400000	0.00001
		0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	Subtracted	6325	85
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5	Subtracted	8126	41482.5
		1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	Divided	5.31521	450.5
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	Subtracted	11621	4294
		0	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	Divided	2.55362	5865
		1	hbs1-like. [refseq;acc:nm_006620]	322	Subtracted	107	215
		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). [swissprot;acc:o60476]	28	Divided	1.86667	15
	Squared	0	histone h4. [swissprot;acc:p02304]	345123	Subtracted	71500	273623
		0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	Divided	561325	5.61325
		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). [swissprot;acc:o60476]	263351	Subtracted	143938	407289
		1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07	Divided	28.2513	48.0356
	Rooted	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707	Subtracted	50.8706	9.20014
		0	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	Divided	1240970	12.4097
		1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	Divided	2.30547	21.225
		1		48.9336	Subtracted	27.7086	21.225
3	Measured	0	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	Subtracted	4196.8	23818.1
		0	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	Divided	10900000	0.00001
		1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	33356.5	Subtracted	8126	41482.5
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	698.5	Divided	3.71868	2597.5
	Ranked	0	cab2. [refseq;acc:nm_033419]	10950	Subtracted	10916	21866
		0	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	Divided	2.47638	4475.84
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	Divided	1.86667	15
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]	232	Subtracted	105	337
	Squared	0	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628	Subtracted	35348	135280
		0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	Divided	561325	5.61325
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	263351	Subtracted	143938	407289
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	115.48	Divided	13.8285	1596.92
	Rooted	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565	Subtracted	30.0631	36.9188
		0	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	Divided	1240970	12.4097
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	Divided	1.92839	50.9657
		1		26.4292	Subtracted	24.5365	50.9657
4	Measured	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	Divided	8900000	0.00001
4	Measured	0	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	21730	Subtracted	3026	18704

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/