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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Rank Value Type Gene Filtered description Network Comparison Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 38536 in total 
Network Comparison Type	Divided

Rank	Value Type	Filtered	description	Interaction Map	green	red	network_comparison	
4	Measured	1	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	698.5	2597.5	3.71868	
4	Measured	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	543.5	2399.5	4.4149	
4	Ranked	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	High confidence	21883	8906	2.45711	
4	Ranked	0	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721]	Low confidence	20617	9607	2.14604	
4	Ranked	1	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	330	223	1.47982	
4	Ranked	1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	High confidence	28	15	1.86667	
4	Squared	0	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	Low confidence	0.823905	0.00001	82390.5	
4	Squared	0	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	High confidence	2.81207	0.00001	281207	
4	Squared	1	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	115.48	1596.92	13.8285	
4	Squared	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	69.9153	1362.75	19.4914	
4	Rooted	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Low confidence	9.43398	0.00001	943398	
4	Rooted	0	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	High confidence	10.4403	0.00001	1044030	
4	Rooted	1	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	26.4292	50.9657	1.92839	
4	Rooted	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	23.3131	48.9847	2.10117	
5	Measured	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	89	0.00001	8900000	
5	Measured	0	jumonji protein. [source:swissprot;acc:q92833]	Low confidence	17.5166	0.00001	1751660	
5	Measured	1	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	339.5	1153.5	3.39764	
5	Measured	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	2113.5	736.5	2.86965	
5	Ranked	0	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	High confidence	11965.7	5510.5	2.17144	
5	Ranked	0	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [source:swissprot;acc:o14607]	Low confidence	19873	10889.4	1.82499	
5	Ranked	1	cytohesin 4. [source:swissprot;acc:q9uia0]	High confidence	28	15	1.86667	
5	Ranked	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	330	223	1.47982	
5	Squared	0	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	Low confidence	0.00001	0.324024	32402.4	
5	Squared	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	High confidence	1.87479	0.00001	187479	
5	Squared	1	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	27.2805	314.926	11.544	
5	Squared	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	1057.25	128.386	8.23493	
5	Rooted	0	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	Low confidence	7.68115	0.00001	768115	
5	Rooted	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	High confidence	9.43398	0.00001	943398	
5	Rooted	1	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	18.4255	33.9632	1.84327	
5	Rooted	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	45.9728	27.1385	1.69401	
6	Measured	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	High confidence	89	0.00001	8900000	
6	Measured	0	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Low confidence	0.00001	13	1300000	
6	Measured	1	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	339.5	1153.5	3.39764	
6	Measured	1	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	2113.5	736.5	2.86965	
6	Ranked	0	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Low confidence	9583.37	5575.71	1.71877	
6	Ranked	0	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	High confidence	15339.2	7523	2.03897	
6	Ranked	1	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	High confidence	28	15	1.86667	
6	Ranked	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	240	318	1.325	
6	Squared	0	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [source:refseq;acc:nm_004267]	Low confidence	0.00001	0.324024	32402.4	
6	Squared	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	1.87479	0.00001	187479	
6	Squared	1	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	27.2805	314.926	11.544	
6	Squared	1	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	1057.25	128.386	8.23493	
6	Rooted	0	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [source:refseq;acc:nm_021615]	Low confidence	0.00001	6.08276	608276	
6	Rooted	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	9.43398	0.00001	943398	
6	Rooted	1	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	18.4255	33.9632	1.84327	
6	Rooted	1	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	45.9728	27.1385	1.69401	
7	Measured	0	sedlin. [source:swissprot;acc:o14582]	High confidence	43	0.00001	4300000	
7	Measured	0	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	Low confidence	0.00001	2.31962	231962	
7	Measured	1	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Low confidence	2113.5	736.5	2.86965	
7	Measured	1	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]	High confidence	339.5	1153.5	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/