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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 844 to 893 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
106	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Rooted	1	60.8692	77.7165	1.27678
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Squared	0	299.137	144.414	2.07139
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Measured		1251.66	858.525	1.45792
	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	Rooted		5.47723	7.07107	1.29099
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]	Ranked	1	252.329	202.004	1.24913
107	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Measured		4266.04	5843.51	1.36977
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Squared		407289	263351	1.54656
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Rooted		60.875	77.7152	1.27664
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Ranked		252.309	201.998	1.24907
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Measured	0	326.677	472.605	1.4467
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Rooted		22.2259	17.2182	1.29084
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Squared		4141.27	2000.69	2.06992
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Ranked		11853.5	9808.86	1.20845
108	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Measured		292	421	1.44178
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Rooted		13.7191	17.6786	1.28861
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Measured	1	4366.44	5899.76	1.35116
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Ranked		252.296	201.995	1.24902
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Squared		19321	12542.6	1.54043
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Ranked	0	10585.3	12769.1	1.2063
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Squared	0	795.24	1645.86	2.06964
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Rooted	1	49.2925	62.397	1.26585
109	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Measured	0	100	144	1.44
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Ranked	0	14466.8	12031.7	1.20239
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Ranked	1	266.933	333.281	1.24856
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Squared	1	19321	12542.6	1.54043
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Rooted	0	2.64575	3.38392	1.279
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Measured	1	4366.44	5899.76	1.35116
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Rooted	1	49.2923	62.3969	1.26585
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Squared	0	16.4056	33.4891	2.04132
110	deltex 2. [refseq;acc:nm_020892]	Ranked	1	333.144	267.393	1.2459
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Ranked	0	12584.5	10470.6	1.20189
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Squared	1	19321	12542.6	1.54043
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Measured	1	4366.44	5899.76	1.35116
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Rooted	0	7.7419	6.06104	1.27732
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Measured	0	1833	2637	1.43863
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Rooted	1	49.293	62.3973	1.26585
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	Squared	0	16.4056	33.4891	2.04132
111	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Ranked	1	332.925	267.274	1.24563
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Squared		19321	12542.6	1.54043
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Measured		4366.44	5899.76	1.35116
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Ranked	0	9940.69	11929	1.20002
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured		2965.5	2063	1.43747
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Rooted		21.0524	16.4963	1.27619
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Rooted	1	49.2923	62.3969	1.26585
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	Squared	0	16.4056	33.4891	2.04132
112	40s ribosomal protein s26. [swissprot;acc:p02383]	Ranked		14269.7	17098	1.1982
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Rooted		22.4608	17.665	1.27149
	lats homolog 1. [refseq;acc:nm_004690]	Measured		160	112.25	1.42539
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Squared		138.269	68.9705	2.00476
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Squared	1	19321	12542.6	1.54043

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/