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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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