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 Filtered Gene description Network Comparison Type Interaction Map red green 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	red	green	network_comparison	
4	Measured	1	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	2597.5	698.5	3.71868	
4	Measured	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	2399.5	543.5	4.4149	
4	Ranked	0	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	High confidence	8906	21883	2.45711	
4	Ranked	0	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [source:swissprot;acc:q04721]	Low confidence	9607	20617	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	223	330	1.47982	
4	Ranked	1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	High confidence	15	28	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	0.00001	0.823905	82390.5	
4	Squared	0	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	High confidence	0.00001	2.81207	281207	
4	Squared	1	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	1596.92	115.48	13.8285	
4	Squared	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	1362.75	69.9153	19.4914	
4	Rooted	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Low confidence	0.00001	9.43398	943398	
4	Rooted	0	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	High confidence	0.00001	10.4403	1044030	
4	Rooted	1	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	50.9657	26.4292	1.92839	
4	Rooted	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	48.9847	23.3131	2.10117	
5	Measured	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	0.00001	89	8900000	
5	Measured	0	jumonji protein. [source:swissprot;acc:q92833]	Low confidence	0.00001	17.5166	1751660	
5	Measured	1	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	1153.5	339.5	3.39764	
5	Measured	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	736.5	2113.5	2.86965	
5	Ranked	0	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	High confidence	5510.5	11965.7	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	10889.4	19873	1.82499	
5	Ranked	1	cytohesin 4. [source:swissprot;acc:q9uia0]	High confidence	15	28	1.86667	
5	Ranked	1	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	223	330	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	0.324024	0.00001	32402.4	
5	Squared	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	High confidence	0.00001	1.87479	187479	
5	Squared	1	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	314.926	27.2805	11.544	
5	Squared	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	128.386	1057.25	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	0.00001	7.68115	768115	
5	Rooted	0	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	High confidence	0.00001	9.43398	943398	
5	Rooted	1	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	33.9632	18.4255	1.84327	
5	Rooted	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	27.1385	45.9728	1.69401	
6	Measured	0	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	High confidence	0.00001	89	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	13	0.00001	1300000	
6	Measured	1	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	1153.5	339.5	3.39764	
6	Measured	1	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	736.5	2113.5	2.86965	
6	Ranked	0	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Low confidence	5575.71	9583.37	1.71877	
6	Ranked	0	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	High confidence	7523	15339.2	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	15	28	1.86667	
6	Ranked	1	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	318	240	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	0.324024	0.00001	32402.4	
6	Squared	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	0.00001	1.87479	187479	
6	Squared	1	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	314.926	27.2805	11.544	
6	Squared	1	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	128.386	1057.25	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	6.08276	0.00001	608276	
6	Rooted	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	0.00001	9.43398	943398	
6	Rooted	1	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	33.9632	18.4255	1.84327	
6	Rooted	1	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	27.1385	45.9728	1.69401	
7	Measured	0	sedlin. [source:swissprot;acc:o14582]	High confidence	0.00001	43	4300000	
7	Measured	0	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [source:refseq;acc:nm_007063]	Low confidence	2.31962	0.00001	231962	
7	Measured	1	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Low confidence	736.5	2113.5	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	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/