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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
1	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	215	322	107	
1	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Divided	10	24	2.4	
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]	Divided	15	28	1.86667	
2	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	215	322	107	
3	PSCD1	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Divided	15	28	1.86667	
3	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	337	232	105	
4	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Divided	15	28	1.86667	
4	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	337	232	105	
5	PSCD4	cytohesin 4. [source:swissprot;acc:q9uia0]	Divided	15	28	1.86667	
5	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	212	309	97	
6	ATPBD1C	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	212	309	97	
6	PSCD3	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	
7	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	215	322	1.49767	
7	UFC1	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Subtracted	288.754	212.554	76.2	
8	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Divided	215	322	1.49767	
8	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Subtracted	288	362	74	
9	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Subtracted	288	362	74	
9	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Divided	212	309	1.45755	
10	ATPBD1C	protein x 0004. [source:refseq;acc:nm_016301]	Divided	212	309	1.45755	
10	SMPD2	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	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	337	232	1.45259	
11	TMEM33	db83 protein. [source:swissprot;acc:p57088]	Subtracted	288	362	74	
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	RHOBTB2	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	GNG12	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	UFC1	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Divided	288.754	212.554	1.3585	
14	ATG4A	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	GNG4	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	GNG3	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	MAP1LC3B	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	GNG8	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	MAP1LC3A	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	ATG4B	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Divided	56.7841	75.447	1.32866	
17	GNG5	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	GBE1	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	GNG10	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		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	
19	PYGB	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Divided	185.678	245.247	1.32082	
20	GNG11	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Subtracted	266.868	336.159	69.291	
20	PYGL	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Divided	185.678	245.247	1.32082	
21	MYO15A	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Divided	185.678	245.247	1.32082	
21	TMEM132A	gbp protein isoform a. [source:refseq;acc:nm_017870]	Subtracted	325.586	256.492	69.094	
22	PPP1R14A	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Subtracted	322	253	69	
22	PYGM	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Divided	185.678	245.247	1.32082	
23	MFAP4	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Subtracted	322	253	69	
23	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Divided	58	44	1.31818	
24	PANK1	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Divided	58	44	1.31818	
24	PPP1R14D	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Subtracted	322	253	69	
25	FCN2	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	PANK2	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Divided	58	44	1.31818	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/