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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

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

Results: HTML CSV LaTeX

Showing element 430 to 479 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
108	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Ranked	252.296	201.995	1.24902	
108	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Squared	19321	12542.6	1.54043	
108	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	Rooted	49.2925	62.397	1.26585	
109	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Ranked	266.933	333.281	1.24856	
109	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Squared	19321	12542.6	1.54043	
109	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Measured	4366.44	5899.76	1.35116	
109	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	Rooted	49.2923	62.3969	1.26585	
110	deltex 2. [source:refseq;acc:nm_020892]	Ranked	333.144	267.393	1.2459	
110	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [source:swissprot;acc:p13535]	Squared	19321	12542.6	1.54043	
110	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Measured	4366.44	5899.76	1.35116	
110	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Rooted	49.293	62.3973	1.26585	
111	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Ranked	332.925	267.274	1.24563	
111	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Squared	19321	12542.6	1.54043	
111	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Measured	4366.44	5899.76	1.35116	
111	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Rooted	49.2923	62.3969	1.26585	
112	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Squared	19321	12542.6	1.54043	
112	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Ranked	332.874	267.246	1.24557	
112	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Measured	4366.44	5899.76	1.35116	
112	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Rooted	49.3267	62.4167	1.26537	
113	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Rooted	80.4705	101.526	1.26165	
113	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Measured	4366.44	5899.76	1.35116	
113	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Ranked	332.874	267.246	1.24557	
113	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Squared	19321	12542.6	1.54043	
114	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Rooted	80.4705	101.526	1.26165	
114	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Measured	4300.47	5807.72	1.35048	
114	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Ranked	332.874	267.246	1.24557	
114	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Squared	19321	12542.6	1.54043	
115	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Measured	21185	28492	1.34491	
115	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Squared	19321	12542.6	1.54043	
115	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Ranked	332.874	267.246	1.24557	
115	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Rooted	80.4705	101.526	1.26165	
116	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Rooted	80.4705	101.526	1.26165	
116	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	Ranked	268.565	334.483	1.24545	
116	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Squared	19321	12542.6	1.54043	
116	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Measured	21185	28492	1.34491	
117	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Squared	211446	137422	1.53866	
117	neuralized-like. [source:refseq;acc:nm_004210]	Ranked	332.326	266.948	1.24491	
117	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Measured	21185	28492	1.34491	
117	transcription factor jun-b. [source:swissprot;acc:p17275]	Rooted	63.4173	79.5311	1.25409	
118	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Rooted	50.3065	62.9788	1.2519	
118	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Ranked	284.753	228.934	1.24382	
118	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Measured	21185	28492	1.34491	
118	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Squared	210445	136779	1.53858	
119	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Squared	210335	136716	1.53848	
119	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Measured	21185	28492	1.34491	
119	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Ranked	318.982	259.004	1.23157	
119	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Rooted	50.3247	62.9892	1.25166	
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Measured	5136.78	6895.98	1.34247	
120	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Rooted	50.3333	62.9942	1.25154	
120	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Squared	210199	136638	1.53836	

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/