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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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 Filtered Gene description green Interaction Map Network Comparison Type network_comparison red

Results: HTML CSV LaTeX

Showing element 101 to 150 of 14920 in total

Interaction Map

: High confidence
Network Comparison Type

: Divided

Rank	Value Type	Filtered	description	green	network_comparison	red
13	Squared	0	dok-like protein. [refseq;acc:nm_024872]	0.00001	28994.1	0.289941
	Squared	1	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	388.696	10.3414	37.5863
	Rooted	0	dok-like protein. [refseq;acc:nm_024872]	0.00001	591608	5.91608
	Rooted	1	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	35.798	1.79326	19.9625
14	Measured	0	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	6.50325	20.0687	130.512
	Measured	1	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1281.5	3.21581	398.5
	Ranked	0	dystrophin. [swissprot;acc:p11532]	18054.8	1.76446	10232.5
	Ranked	1	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	75.3531	1.32952	56.6768
	Squared	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	19295.9	11098	1.73869
	Squared	1	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	388.696	10.3414	37.5863
	Rooted	0	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). [swissprot;acc:o00750]	4.24264	424264	0.00001
	Rooted	1	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	35.798	1.79326	19.9625
15	Measured	0	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). [swissprot;acc:o14521]	156	15.6	10
	Measured	1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	871	3.06659	2671
	Ranked	0	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). [swissprot;acc:o14521]	11267	1.72211	19403
	Ranked	1	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	75.3948	1.32914	56.7244
	Squared	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	19295.9	11098	1.73869
	Squared	1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	179.56	9.40399	1688.58
	Rooted	0	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	0.00001	424264	4.24264
	Rooted	1	gbp protein isoform a. [refseq;acc:nm_017870]	42.4773	1.77158	23.9771
16	Measured	0	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	15	15	1
	Measured	1	protein x 0004. [refseq;acc:nm_016301]	871	3.06659	2671
	Ranked	0	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	20670.6	1.69839	12170.7
	Ranked	1	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	75.3954	1.32913	56.7252
	Squared	0	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). [swissprot;acc:o00750]	0.0766864	7668.64	0.00001
	Squared	1	protein x 0004. [refseq;acc:nm_016301]	179.56	9.40399	1688.58
	Rooted	0	serpin b12. [swissprot;acc:q96p63]	1.18697	8.67149	10.2928
	Rooted	1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	29.5127	1.75117	51.6817
17	Measured	0	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	58	14.8103	859
	Measured	1	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	1365	2.96739	460
	Ranked	0	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	6812	1.69451	11543
	Ranked	1	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	75.447	1.32866	56.7841
	Squared	0	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	0.00001	7668.64	0.0766864
	Squared	1	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	441	8.80542	50.0828
	Rooted	0	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	1.2188	8.45791	10.3085
	Rooted	1	protein x 0004. [refseq;acc:nm_016301]	29.5127	1.75117	51.6817
18	Measured	0	60s ribosomal protein l37a. [swissprot;acc:p12751]	26.1599	11.6763	305.45
	Measured	1	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1865.5	2.75351	677.5
	Ranked	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	13216	1.68629	22286
	Ranked	1	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	245.247	1.32082	185.678
	Squared	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0.52284	841.001	439.709
	Squared	1	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	823.69	7.58176	108.641
	Rooted	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	6.52932	9.20014
	Rooted	1	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	36.9459	1.72261	21.4476
19	Measured	0	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	26.1599	11.6763	305.45
	Measured	1	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1865.5	2.75351	677.5
	Ranked	0	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	13216	1.68629	22286
	Ranked	1	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	245.247	1.32082	185.678
	Squared	0	serpin b12. [swissprot;acc:q96p63]	0.0289898	813.196	23.5744
	Squared	1	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	823.69	7.58176	108.641

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/