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.

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

Results: HTML CSV LaTeX

Showing element 425 to 474 of 7460 in total

Value Type

: Measured
Interaction Map

: High confidence

description	Rank	Network Comparison Type	Filtered	red	network_comparison	green
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	1280	Subtracted	1	6036.22	476.42	6512.64
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	1354	Divided		6036.22	1.07893	6512.64
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	975	Subtracted		5791.82	549.04	6340.86
	1020	Divided		5791.82	1.0948	6340.86
actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]	1778	Divided		5386.37	1.06656	5744.89
	1916	Subtracted			358.52
actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]	1783	Divided			1.06656
	1921	Subtracted			358.52
actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]	1786	Divided			1.06656
	1924	Subtracted			358.52
activated p21cdc42hs kinase. [refseq;acc:nm_005781]	1055	Divided		4757.46	1.09279	5198.91
activated p21cdc42hs kinase. [refseq;acc:nm_005781]	1474	Subtracted		4757.46	441.45	5198.91
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]	932	Subtracted		6281.21	556.4	6837.61
	1146	Divided		6281.21	1.08858	6837.61
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482]	2435	Divided		3669.33	1.03501	3797.78
	2517	Subtracted		3669.33	128.45	3797.78
activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	2160	Divided		5379.55	1.05218	5660.25
	2192	Subtracted		5379.55	280.7	5660.25
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]	3050	Divided		0.00001	1	0.00001
	3050	Subtracted		0	0	0
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]	1585	Subtracted		6858.84	428.43	7287.27
	1917	Divided		6858.84	1.06246	7287.27
acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	2578	Subtracted		6380.61	95.58	6476.19
	2612	Divided		6380.61	1.01498	6476.19
acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	44	Divided	0	45.4292	2.16837	98.5074
	350	Subtracted	0	45.4292	53.0782	98.5074
	1440	Subtracted	1	6296.52	447.33	6743.85
	1620	Divided		6296.52	1.07104	6743.85
acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	119	Subtracted		12998.5	2139.7	15138.2
	380	Divided		12998.5	1.16461	15138.2
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]	1736	Subtracted		6920.71	394.88	7315.59
	2035	Divided		6920.71	1.05706	7315.59
acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424]	1902	Subtracted		6884.69	362.67	7247.36
	2154	Divided		6884.69	1.05268	7247.36
ad24 protein. [refseq;acc:nm_022451]	445	Divided		3753.71	1.14978	4315.95
ad24 protein. [refseq;acc:nm_022451]	911	Subtracted		3753.71	562.24	4315.95
adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]	1526	Subtracted		5916.05	434.48	6350.53
	1530	Divided		5916.05	1.07344	6350.53
adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567]	2064	Divided		5548.79	1.05632	5861.31
	2100	Subtracted		5548.79	312.52	5861.31
adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747]	2059	Divided		5552.69	1.0564	5865.84
	2087	Subtracted		5552.69	313.15	5865.84
adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843]	2062	Divided		5552.7	1.0564	5865.85
	2090	Subtracted		5552.7	313.15	5865.85
adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382]	2061	Divided		5552.69	1.0564	5865.84
	2089	Subtracted		5552.69	313.15	5865.84
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	60	Divided	0	47.4756	1.8441	87.5499
	383	Subtracted	0	47.4756	40.0743	87.5499
	2058	Divided	1	5552.69	1.0564	5865.84
	2086	Subtracted	1	5552.69	313.15	5865.84

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/