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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map	High confidence

Rank	Value Type	description	Network Comparison Type	Filtered	red	green	network_comparison	
1	Measured	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Subtracted	0	85	6410	6325	
1	Measured	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). [source:swissprot;acc:o60476]	Subtracted	1	41482.5	33356.5	8126	
1	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Divided	0	364	0.00001	36400000	
1	Measured	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	1	450.5	2394.5	5.31521	
1	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Divided	0	4294	15915	3.70633	
1	Ranked	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	1	215	322	107	
1	Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Subtracted	0	8906	21883	12977	
1	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Divided	1	10	24	2.4	
1	Squared	cab2. [source:refseq;acc:nm_033419]	Divided	0	0.00001	7.16592	716592	
1	Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Subtracted	0	232467	160184	72283	
1	Squared	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	1	468498	322755	145743	
1	Squared	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	1	48.0356	1357.07	28.2513	
1	Rooted	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Subtracted	0	9.20014	60.0707	50.8706	
1	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Divided	0	19.0788	0.00001	1907880	
1	Rooted	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	1	21.225	48.9336	2.30547	
1	Rooted	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	1	21.225	48.9336	27.7086	
2	Measured	cab2. [source:refseq;acc:nm_033419]	Divided	0	0.00001	174	17400000	
2	Measured	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	1	41482.5	33356.5	8126	
2	Measured	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Subtracted	0	85	6410	6325	
2	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	1	450.5	2394.5	5.31521	
2	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Subtracted	0	4294	15915	11621	
2	Ranked	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	1	215	322	107	
2	Ranked	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). [source:swissprot;acc:o60476]	Divided	1	15	28	1.86667	
2	Ranked	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Divided	0	5865	14977	2.55362	
2	Squared	histone h4. [source:swissprot;acc:p02304]	Subtracted	0	273623	345123	71500	
2	Squared	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). [source:swissprot;acc:o60476]	Subtracted	1	407289	263351	143938	
2	Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Divided	0	5.61325	0.00001	561325	
2	Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	1	48.0356	1357.07	28.2513	
2	Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Subtracted	0	9.20014	60.0707	50.8706	
2	Rooted	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Divided	0	12.4097	0.00001	1240970	
2	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	1	21.225	48.9336	2.30547	
2	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	1	21.225	48.9336	27.7086	
3	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	1	41482.5	33356.5	8126	
3	Measured	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	1	2597.5	698.5	3.71868	
3	Measured	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Subtracted	0	23818.1	19621.3	4196.8	
3	Measured	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Divided	0	0.00001	109	10900000	
3	Ranked	cab2. [source:refseq;acc:nm_033419]	Subtracted	0	21866	10950	10916	
3	Ranked	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Divided	1	15	28	1.86667	
3	Ranked	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Divided	0	4475.84	11083.9	2.47638	
3	Ranked	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	1	337	232	105	
3	Squared	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Subtracted	0	135280	170628	35348	
3	Squared	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	1	407289	263351	143938	
3	Squared	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	1	1596.92	115.48	13.8285	
3	Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Divided	0	5.61325	0.00001	561325	
3	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Subtracted	0	36.9188	6.85565	30.0631	
3	Rooted	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	1	50.9657	26.4292	1.92839	
3	Rooted	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	1	50.9657	26.4292	24.5365	
3	Rooted	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Divided	0	12.4097	0.00001	1240970	
4	Measured	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	1	41482.5	33356.5	8126	
4	Measured	hbs1-like. [source:refseq;acc:nm_006620]	Divided	1	2597.5	698.5	3.71868	

Legend:
- Rank is the rank after comparing the two networks
- 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/