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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

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

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/