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 Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 80 to 129 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Rooted	1	19.9625	35.798	1.79326	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Measured	1	398.5	1281.5	3.21581	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Squared	1	37.5863	388.696	10.3414	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Rooted	1	19.9625	35.798	1.79326	
11	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	Ranked	0	11627	6248	1.86092	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Ranked	1	337	232	1.45259	
11	sedlin. [source:swissprot;acc:o14582]	Squared	0	0.00001	0.437633	43763.3	
11	sedlin. [source:swissprot;acc:o14582]	Rooted	0	0.00001	6.55744	655744	
11	serpin b12. [source:swissprot;acc:q96p63]	Measured	0	199.549	5.56738	35.8425	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Measured	1	398.5	1281.5	3.21581	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Squared	1	37.5863	388.696	10.3414	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Rooted	1	19.9625	35.798	1.79326	
12	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	Ranked	0	9429.18	5208.84	1.81023	
12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	Measured	0	199.249	5.71669	34.8539	
12	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Ranked	1	337	232	1.45259	
12	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Squared	0	0.00001	0.437633	43763.3	
12	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Rooted	0	0.00001	6.55744	655744	
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Measured	0	1363	47	29	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Measured	1	398.5	1281.5	3.21581	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Squared	1	37.5863	388.696	10.3414	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Rooted	1	19.9625	35.798	1.79326	
13	dok-like protein. [source:refseq;acc:nm_024872]	Squared	0	0.289941	0.00001	28994.1	
13	dok-like protein. [source:refseq;acc:nm_024872]	Rooted	0	5.91608	0.00001	591608	
13	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	Ranked	0	5210.5	9264.5	1.77804	
13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Ranked	1	288.754	212.554	1.3585	
14	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Squared	0	1.73869	19295.9	11098	
14	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	Measured	0	130.512	6.50325	20.0687	
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Ranked	1	56.6768	75.3531	1.32952	
14	dystrophin. [source:swissprot;acc:p11532]	Ranked	0	10232.5	18054.8	1.76446	
14	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	Rooted	0	0.00001	4.24264	424264	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Measured	1	398.5	1281.5	3.21581	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Squared	1	37.5863	388.696	10.3414	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Rooted	1	19.9625	35.798	1.79326	
15	gbp protein isoform a. [source:refseq;acc:nm_017870]	Rooted	1	23.9771	42.4773	1.77158	
15	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Squared	0	1.73869	19295.9	11098	
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Ranked	1	56.7244	75.3948	1.32914	
15	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	Rooted	0	4.24264	0.00001	424264	
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Measured	0	10	156	15.6	
15	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Ranked	0	19403	11267	1.72211	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Measured	1	2671	871	3.06659	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Squared	1	1688.58	179.56	9.40399	
16	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	Ranked	0	12170.7	20670.6	1.69839	
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Ranked	1	56.7252	75.3954	1.32913	
16	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	Squared	0	0.00001	0.0766864	7668.64	
16	protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	Measured	0	1	15	15	
16	protein x 0004. [source:refseq;acc:nm_016301]	Measured	1	2671	871	3.06659	
16	protein x 0004. [source:refseq;acc:nm_016301]	Squared	1	1688.58	179.56	9.40399	
16	serpin b12. [source:swissprot;acc:q96p63]	Rooted	0	10.2928	1.18697	8.67149	
16	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Rooted	1	51.6817	29.5127	1.75117	
17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Ranked	1	56.7841	75.447	1.32866	

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/