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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

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

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/