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 Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 25 to 74 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Ranked	1	15	28	1.86667	
4	hbs1-like. [source:refseq;acc:nm_006620]	Measured	1	2597.5	698.5	3.71868	
4	hbs1-like. [source:refseq;acc:nm_006620]	Squared	1	1596.92	115.48	13.8285	
4	hbs1-like. [source:refseq;acc:nm_006620]	Rooted	1	50.9657	26.4292	1.92839	
4	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Measured	0	0.00001	89	8900000	
4	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Ranked	0	8906	21883	2.45711	
4	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Squared	0	0.00001	2.81207	281207	
4	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	Rooted	0	0.00001	10.4403	1044030	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Ranked	1	15	28	1.86667	
5	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Squared	0	0.00001	1.87479	187479	
5	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Rooted	0	0.00001	9.43398	943398	
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Measured	0	0.00001	89	8900000	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Measured	1	1153.5	339.5	3.39764	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Squared	1	314.926	27.2805	11.544	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Rooted	1	33.9632	18.4255	1.84327	
5	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Ranked	0	5510.5	11965.7	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	15	28	1.86667	
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Measured	0	0.00001	89	8900000	
6	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Squared	0	0.00001	1.87479	187479	
6	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Rooted	0	0.00001	9.43398	943398	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Measured	1	1153.5	339.5	3.39764	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Squared	1	314.926	27.2805	11.544	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Rooted	1	33.9632	18.4255	1.84327	
6	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	Ranked	0	7523	15339.2	2.03897	
7	cab2. [source:refseq;acc:nm_033419]	Ranked	0	21866	10950	1.99689	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Ranked	1	215	322	1.49767	
7	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Squared	0	0.00001	1.87479	187479	
7	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Rooted	0	0.00001	9.43398	943398	
7	sedlin. [source:swissprot;acc:o14582]	Measured	0	0.00001	43	4300000	
7	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]	Measured	1	1153.5	339.5	3.39764	
7	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]	Squared	1	314.926	27.2805	11.544	
7	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]	Rooted	1	33.9632	18.4255	1.84327	
8	db83 protein. [source:swissprot;acc:p57088]	Measured	1	1153.5	339.5	3.39764	
8	db83 protein. [source:swissprot;acc:p57088]	Squared	1	314.926	27.2805	11.544	
8	db83 protein. [source:swissprot;acc:p57088]	Rooted	1	33.9632	18.4255	1.84327	
8	ero1-like. [source:refseq;acc:nm_014584]	Squared	0	1.59148	0.00001	159148	
8	ero1-like. [source:refseq;acc:nm_014584]	Rooted	0	9.05539	0.00001	905539	
8	hbs1-like. [source:refseq;acc:nm_006620]	Ranked	1	215	322	1.49767	
8	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Ranked	0	11525	21888	1.89918	
8	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Measured	0	0.00001	43	4300000	
9	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Measured	0	85	6410	75.4118	
9	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Squared	0	0.852071	0.00001	85207.1	
9	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Rooted	0	7.74597	0.00001	774597	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Measured	1	398.5	1281.5	3.21581	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Squared	1	37.5863	388.696	10.3414	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Rooted	1	19.9625	35.798	1.79326	
9	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Ranked	0	11525	21888	1.89918	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Ranked	1	212	309	1.45755	
10	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	Ranked	0	7509.39	14178.1	1.88805	
10	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]	Squared	0	0.00001	0.823905	82390.5	

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/