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 Value Type Gene description Network Comparison Type Filtered 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). [swissprot;acc:p09017]	0	High confidence	89	0.00001	8900000
	Measured	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1	Low confidence	543.5	2399.5	4.4149
	Ranked	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		Low confidence	330	223	1.47982
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		High confidence	28	15	1.86667
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	High confidence	21883	8906	2.45711
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		Low confidence	20617	9607	2.14604
	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). [swissprot;acc:q9byb4]		Low confidence	0.823905	0.00001	82390.5
		hbs1-like. [refseq;acc:nm_006620]	1	High confidence	115.48	1596.92	13.8285
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1	Low confidence	69.9153	1362.75	19.4914
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	High confidence	2.81207	0.00001	281207
	Rooted	hbs1-like. [refseq;acc:nm_006620]	1	High confidence	26.4292	50.9657	1.92839
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	Low confidence	9.43398	0.00001	943398
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1	Low confidence	23.3131	48.9847	2.10117
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	High confidence	10.4403	0.00001	1044030
5	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		High confidence	89		8900000
		jumonji protein. [swissprot;acc:q92833]		Low confidence	17.5166		1751660
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1	High confidence	339.5	1153.5	3.39764
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Low confidence	2113.5	736.5	2.86965
	Ranked	cytohesin 4. [swissprot;acc:q9uia0]		High confidence	28	15	1.86667
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]		Low confidence	330	223	1.47982
		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	0	High confidence	11965.7	5510.5	2.17144
		ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]		Low confidence	19873	10889.4	1.82499
	Squared	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]		Low confidence	0.00001	0.324024	32402.4
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		High confidence	1.87479	0.00001	187479
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1	High confidence	27.2805	314.926	11.544
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1	Low confidence	1057.25	128.386	8.23493
	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). [swissprot;acc:q9byb4]	0	Low confidence	7.68115	0.00001	768115
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	High confidence	9.43398	0.00001	943398
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	1	High confidence	18.4255	33.9632	1.84327
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1	Low confidence	45.9728	27.1385	1.69401
6	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	High confidence	89	0.00001	8900000
		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0	Low confidence	0.00001	13	1300000
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1	High confidence	339.5	1153.5	3.39764
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]		Low confidence	2113.5	736.5	2.86965
	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		High confidence	28	15	1.86667
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Low confidence	240	318	1.325
		trinucleotide repeat containing 15. [refseq;acc:nm_015575]	0	Low confidence	9583.37	5575.71	1.71877
		ubiquitin protein ligase. [refseq;acc:nm_130466]		High confidence	15339.2	7523	2.03897
	Squared	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		Low confidence	0.00001	0.324024	32402.4
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		High confidence	1.87479	0.00001	187479
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1	High confidence	27.2805	314.926	11.544
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	1	Low confidence	1057.25	128.386	8.23493
	Rooted	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	0	Low confidence	0.00001	6.08276	608276
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	High confidence	9.43398	0.00001	943398
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	1	High confidence	18.4255	33.9632	1.84327
		oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]		Low confidence	45.9728	27.1385	1.69401
7	Measured	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]		Low confidence	2113.5	736.5	2.86965
		sedlin. [swissprot;acc:o14582]	0	High confidence	43	0.00001	4300000
		sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	1	High confidence	339.5	1153.5	3.39764
		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	0	Low confidence	0.00001	2.31962	231962

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/