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 Value Type description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total 
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison	
1	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	0	364	0.00001	36400000	
1	Measured	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	1	450.5	2394.5	5.31521	
1	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	0	4294	15915	3.70633	
1	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	1	10	24	2.4	
1	Squared	cab2. [source:refseq;acc:nm_033419]	0	0.00001	7.16592	716592	
1	Squared	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	1	48.0356	1357.07	28.2513	
1	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	0	19.0788	0.00001	1907880	
1	Rooted	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	1	21.225	48.9336	2.30547	
2	Measured	cab2. [source:refseq;acc:nm_033419]	0	0.00001	174	17400000	
2	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	1	450.5	2394.5	5.31521	
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]	1	15	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]	0	5865	14977	2.55362	
2	Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	0	5.61325	0.00001	561325	
2	Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	1	48.0356	1357.07	28.2513	
2	Rooted	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	0	12.4097	0.00001	1240970	
2	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	1	21.225	48.9336	2.30547	
3	Measured	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	1	2597.5	698.5	3.71868	
3	Measured	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	0	0.00001	109	10900000	
3	Ranked	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	1	15	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]	0	4475.84	11083.9	2.47638	
3	Squared	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	1	1596.92	115.48	13.8285	
3	Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	0	5.61325	0.00001	561325	
3	Rooted	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	1	50.9657	26.4292	1.92839	
3	Rooted	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	0	12.4097	0.00001	1240970	
4	Measured	hbs1-like. [source:refseq;acc:nm_006620]	1	2597.5	698.5	3.71868	
4	Measured	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	0	0.00001	89	8900000	
4	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	1	15	28	1.86667	
4	Ranked	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	0	8906	21883	2.45711	
4	Squared	hbs1-like. [source:refseq;acc:nm_006620]	1	1596.92	115.48	13.8285	
4	Squared	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	0	0.00001	2.81207	281207	
4	Rooted	hbs1-like. [source:refseq;acc:nm_006620]	1	50.9657	26.4292	1.92839	
4	Rooted	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	0	0.00001	10.4403	1044030	
5	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	0	0.00001	89	8900000	
5	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	1	1153.5	339.5	3.39764	
5	Ranked	cytohesin 4. [source:swissprot;acc:q9uia0]	1	15	28	1.86667	
5	Ranked	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	0	5510.5	11965.7	2.17144	
5	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	0	0.00001	1.87479	187479	
5	Squared	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	1	314.926	27.2805	11.544	
5	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	0	0.00001	9.43398	943398	
5	Rooted	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	1	33.9632	18.4255	1.84327	
6	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	0	0.00001	89	8900000	
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	1	1153.5	339.5	3.39764	
6	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	1	15	28	1.86667	
6	Ranked	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	0	7523	15339.2	2.03897	
6	Squared	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	0	0.00001	1.87479	187479	
6	Squared	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	1	314.926	27.2805	11.544	
6	Rooted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	0	0.00001	9.43398	943398	
6	Rooted	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	1	33.9632	18.4255	1.84327	
7	Measured	sedlin. [source:swissprot;acc:o14582]	0	0.00001	43	4300000	
7	Measured	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]	1	1153.5	339.5	3.39764	

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/