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 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Ranked	0	4294	15915	3.70633	
1	cab2. [source:refseq;acc:nm_033419]	Squared	0	0.00001	7.16592	716592	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Measured	0	364	0.00001	36400000	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Rooted	0	19.0788	0.00001	1907880	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Ranked	1	10	24	2.4	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Measured	1	450.5	2394.5	5.31521	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Squared	1	48.0356	1357.07	28.2513	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Rooted	1	21.225	48.9336	2.30547	
2	cab2. [source:refseq;acc:nm_033419]	Measured	0	0.00001	174	17400000	
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	1	15	28	1.86667	
2	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Ranked	0	5865	14977	2.55362	
2	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Squared	0	5.61325	0.00001	561325	
2	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Rooted	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	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	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	1	21.225	48.9336	2.30547	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Ranked	1	15	28	1.86667	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Measured	1	2597.5	698.5	3.71868	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Squared	1	1596.92	115.48	13.8285	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Rooted	1	50.9657	26.4292	1.92839	
3	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Ranked	0	4475.84	11083.9	2.47638	
3	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Measured	0	0.00001	109	10900000	
3	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Squared	0	5.61325	0.00001	561325	
3	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Rooted	0	12.4097	0.00001	1240970	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Ranked	1	15	28	1.86667	
4	hbs1-like. [source:refseq;acc:nm_006620]	Measured	1	2597.5	698.5	3.71868	
4	hbs1-like. [source:refseq;acc:nm_006620]	Squared	1	1596.92	115.48	13.8285	
4	hbs1-like. [source:refseq;acc:nm_006620]	Rooted	1	50.9657	26.4292	1.92839	
4	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Measured	0	0.00001	89	8900000	
4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Ranked	0	8906	21883	2.45711	
4	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Squared	0	0.00001	2.81207	281207	
4	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Rooted	0	0.00001	10.4403	1044030	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Ranked	1	15	28	1.86667	
5	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Squared	0	0.00001	1.87479	187479	
5	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Rooted	0	0.00001	9.43398	943398	
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Measured	0	0.00001	89	8900000	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Measured	1	1153.5	339.5	3.39764	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Squared	1	314.926	27.2805	11.544	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Rooted	1	33.9632	18.4255	1.84327	
5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Ranked	0	5510.5	11965.7	2.17144	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Ranked	1	15	28	1.86667	
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Measured	0	0.00001	89	8900000	
6	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Squared	0	0.00001	1.87479	187479	
6	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Rooted	0	0.00001	9.43398	943398	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Measured	1	1153.5	339.5	3.39764	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Squared	1	314.926	27.2805	11.544	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Rooted	1	33.9632	18.4255	1.84327	
6	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	Ranked	0	7523	15339.2	2.03897	
7	cab2. [source:refseq;acc:nm_033419]	Ranked	0	21866	10950	1.99689	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Ranked	1	215	322	1.49767	

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/