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.


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

Rank	description	Value Type	Filtered	green	red	network_comparison	
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Ranked	0	15915	4294	3.70633	
1	cab2. [source:refseq;acc:nm_033419]	Squared	0	7.16592	0.00001	716592	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Measured	0	0.00001	364	36400000	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Rooted	0	0.00001	19.0788	1907880	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Ranked	1	24	10	2.4	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Measured	1	2394.5	450.5	5.31521	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Squared	1	1357.07	48.0356	28.2513	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Rooted	1	48.9336	21.225	2.30547	
2	cab2. [source:refseq;acc:nm_033419]	Measured	0	174	0.00001	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	28	15	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	14977	5865	2.55362	
2	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Squared	0	0.00001	5.61325	561325	
2	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Rooted	0	0.00001	12.4097	1240970	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Measured	1	2394.5	450.5	5.31521	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Squared	1	1357.07	48.0356	28.2513	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Rooted	1	48.9336	21.225	2.30547	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Ranked	1	28	15	1.86667	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Measured	1	698.5	2597.5	3.71868	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Squared	1	115.48	1596.92	13.8285	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Rooted	1	26.4292	50.9657	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	11083.9	4475.84	2.47638	
3	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Measured	0	109	0.00001	10900000	
3	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Squared	0	0.00001	5.61325	561325	
3	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Rooted	0	0.00001	12.4097	1240970	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Ranked	1	28	15	1.86667	
4	hbs1-like. [source:refseq;acc:nm_006620]	Measured	1	698.5	2597.5	3.71868	
4	hbs1-like. [source:refseq;acc:nm_006620]	Squared	1	115.48	1596.92	13.8285	
4	hbs1-like. [source:refseq;acc:nm_006620]	Rooted	1	26.4292	50.9657	1.92839	
4	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Measured	0	89	0.00001	8900000	
4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Ranked	0	21883	8906	2.45711	
4	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Squared	0	2.81207	0.00001	281207	
4	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Rooted	0	10.4403	0.00001	1044030	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Ranked	1	28	15	1.86667	
5	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Squared	0	1.87479	0.00001	187479	
5	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Rooted	0	9.43398	0.00001	943398	
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Measured	0	89	0.00001	8900000	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Measured	1	339.5	1153.5	3.39764	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Squared	1	27.2805	314.926	11.544	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Rooted	1	18.4255	33.9632	1.84327	
5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Ranked	0	11965.7	5510.5	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	28	15	1.86667	
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Measured	0	89	0.00001	8900000	
6	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Squared	0	1.87479	0.00001	187479	
6	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Rooted	0	9.43398	0.00001	943398	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Measured	1	339.5	1153.5	3.39764	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Squared	1	27.2805	314.926	11.544	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Rooted	1	18.4255	33.9632	1.84327	
6	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	Ranked	0	15339.2	7523	2.03897	
7	cab2. [source:refseq;acc:nm_033419]	Ranked	0	10950	21866	1.99689	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Ranked	1	322	215	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/