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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 8 to 57 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
4	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	337	232	105	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Divided	15	28	1.86667	
5	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	212	309	97	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Divided	15	28	1.86667	
6	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	212	309	97	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	215	322	1.49767	
7	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Subtracted	288.754	212.554	76.2	
8	hbs1-like. [source:refseq;acc:nm_006620]	Divided	215	322	1.49767	
8	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Subtracted	288	362	74	
9	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Subtracted	288	362	74	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Divided	212	309	1.45755	
10	protein x 0004. [source:refseq;acc:nm_016301]	Divided	212	309	1.45755	
10	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Subtracted	288	362	74	
11	db83 protein. [source:swissprot;acc:p57088]	Subtracted	288	362	74	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	337	232	1.45259	
12	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Subtracted	266.856	336.233	69.377	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	337	232	1.45259	
13	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Subtracted	266.856	336.233	69.377	
13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Divided	288.754	212.554	1.3585	
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Divided	56.6768	75.3531	1.32952	
14	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	Subtracted	266.863	336.191	69.328	
15	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	Subtracted	266.863	336.19	69.327	
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Divided	56.7244	75.3948	1.32914	
16	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Subtracted	266.864	336.184	69.32	
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Divided	56.7252	75.3954	1.32913	
17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Divided	56.7841	75.447	1.32866	
17	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	Subtracted	266.864	336.182	69.318	
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Divided	185.678	245.247	1.32082	
18	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	Subtracted	266.865	336.181	69.316	
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Divided	185.678	245.247	1.32082	
19	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Subtracted	266.865	336.178	69.313	
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Divided	185.678	245.247	1.32082	
20	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Subtracted	266.868	336.159	69.291	
21	gbp protein isoform a. [source:refseq;acc:nm_017870]	Subtracted	325.586	256.492	69.094	
21	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Divided	185.678	245.247	1.32082	
22	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Divided	185.678	245.247	1.32082	
22	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Subtracted	322	253	69	
23	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Divided	58	44	1.31818	
23	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Subtracted	322	253	69	
24	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Divided	58	44	1.31818	
24	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Subtracted	322	253	69	
25	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Subtracted	322	253	69	
25	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Divided	58	44	1.31818	
26	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Divided	58	44	1.31818	
26	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	Subtracted	322	253	69	
27	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Subtracted	267.136	336.077	68.941	
27	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Divided	58	44	1.31818	
28	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Divided	201.949	153.671	1.31416	
28	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	Subtracted	267.136	336.077	68.941	
29	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	Subtracted	267.139	336.075	68.936	

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/