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 1280 to 1329 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
320	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Measured	20911	24908.5	1.19117	
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Ranked	241.892	265.959	1.09949	
321	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Squared	33526	42390.2	1.2644	
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Measured	20911	24908.5	1.19117	
321	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Rooted	55.9231	62.0565	1.10968	
322	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Measured	20911	24908.5	1.19117	
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Ranked	86.7483	78.8995	1.09948	
322	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Squared	33522.8	42384.8	1.26436	
322	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Rooted	60.594	67.2244	1.10942	
323	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Ranked	241.884	265.945	1.09947	
323	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Rooted	50.3803	45.4193	1.10923	
323	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Squared	33514.4	42370.8	1.26426	
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Measured	4620.76	5501.94	1.1907	
324	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Ranked	243.944	268.195	1.09941	
324	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Measured	28136.5	33457.6	1.18912	
324	fad synthetase. [source:refseq;acc:nm_025207]	Rooted	50.3803	45.4193	1.10923	
324	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	Squared	34527.9	43507.9	1.26008	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	Ranked	243.944	268.195	1.09941	
325	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Rooted	50.3803	45.4193	1.10923	
325	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Squared	34506.3	43476	1.25994	
325	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Measured	16177.9	19235.4	1.18899	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	Ranked	241.899	265.924	1.09932	
326	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	Squared	69124.3	54897.4	1.25915	
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Measured	3432.96	4081.21	1.18883	
326	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Rooted	50.3803	45.4193	1.10923	
327	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	Rooted	50.3803	45.4193	1.10923	
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	Ranked	243.817	267.962	1.09903	
327	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Squared	16424.1	20645.8	1.25704	
327	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Measured	16067.4	19094.4	1.18839	
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Ranked	258.437	235.183	1.09888	
328	brain protein 44. [source:swissprot;acc:o95563]	Measured	15999.1	19007.1	1.18801	
328	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Squared	16442.8	20662.7	1.25664	
328	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Rooted	50.3803	45.4193	1.10923	
329	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Rooted	50.3803	45.4193	1.10923	
329	metaxin 2. [source:swissprot;acc:o75431]	Squared	41236	51807	1.25635	
329	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Ranked	312	284	1.09859	
329	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Measured	15999.1	19007.1	1.18801	
330	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Rooted	50.519	45.5497	1.1091	
330	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	Ranked	312	284	1.09859	
330	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Squared	16203.4	20339.9	1.25529	
330	septin 6. [source:swissprot;acc:q14141]	Measured	15959.9	18957.1	1.1878	
331	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Rooted	60.6697	67.2802	1.10896	
331	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Ranked	312	284	1.09859	
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Measured	20287.2	17083.8	1.18751	
331	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Squared	33100.3	41520.6	1.25439	
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Ranked	312	284	1.09859	
332	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Squared	14464.3	18142.8	1.25432	
332	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Measured	5051.16	5975.51	1.183	
332	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Rooted	60.6732	67.2827	1.10894	
333	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Ranked	312	284	1.09859	

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/