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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map	High confidence

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

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/