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 2577 to 2626 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2577	translin. [source:swissprot;acc:q15631]	4979.44	5071.53	1.01849	
2578	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	4979.44	5071.53	1.01849	
2579	polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [source:refseq;acc:nm_005710]	4979.44	5071.53	1.01849	
2580	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	4331.39	4252.8	1.01848	
2581	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	4570.81	4654.97	1.01841	
2582	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	3899.28	3829.53	1.01821	
2583	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	3926.4	3857.88	1.01776	
2584	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [source:swissprot;acc:o75398]	4180.32	4253.46	1.0175	
2585	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	4180.32	4253.46	1.0175	
2586	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	4180.32	4253.46	1.0175	
2587	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	4180.32	4253.46	1.0175	
2588	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	4180.32	4253.46	1.0175	
2589	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	7181.3	7057.99	1.01747	
2590	chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [source:swissprot;acc:p45973]	7551.88	7422.68	1.01741	
2591	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [source:swissprot;acc:q13185]	7550.12	7422.01	1.01726	
2592	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	7169.01	7047.98	1.01717	
2593	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	4921.84	5005.06	1.01691	
2594	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	4921.84	5005.06	1.01691	
2595	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	4921.84	5005.06	1.01691	
2596	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	4921.84	5005.06	1.01691	
2597	ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [source:swissprot;acc:p51669]	8104.84	7970.2	1.01689	
2598	chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [source:swissprot;acc:p23197]	7538.48	7417.58	1.0163	
2599	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	4367.69	4438.77	1.01627	
2600	dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [source:swissprot;acc:p09622]	6185	6283.8	1.01597	
2601	rad50 homolog isoform 1. [source:refseq;acc:nm_005732]	7222.12	7110.74	1.01566	
2602	lim/homeobox protein lhx3. [source:swissprot;acc:q9ubr4]	7571.73	7688.39	1.01541	
2603	lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [source:refseq;acc:nm_001290]	7572.69	7689.04	1.01536	
2604	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	7572.7	7689.04	1.01536	
2605	lim/homeobox protein lhx4. [source:swissprot;acc:q969g2]	7573.83	7689.81	1.01531	
2606	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [source:swissprot;acc:p54577]	4450.84	4517.54	1.01499	
2607	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	6380.61	6476.19	1.01498	
2608	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	6380.6	6476.18	1.01498	
2609	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [source:refseq;acc:nm_052950]	6380.84	6476.41	1.01498	
2610	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	6380.61	6476.19	1.01498	
2611	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	6380.6	6476.18	1.01498	
2612	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	6380.61	6476.19	1.01498	
2613	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	6380.6	6476.18	1.01498	
2614	stromal interaction molecule 2 precursor. [source:swissprot;acc:q9p246]	6380.61	6476.19	1.01498	
2615	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [source:swissprot;acc:q9p286]	6380.61	6476.19	1.01498	
2616	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [source:refseq;acc:nm_020830]	6380.32	6475.92	1.01498	
2617	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [source:swissprot;acc:q9udy4]	5599.85	5683	1.01485	
2618	cab2. [source:refseq;acc:nm_033419]	5599.85	5683	1.01485	
2619	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [source:swissprot;acc:o75953]	5599.85	5683	1.01485	
2620	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [source:swissprot;acc:p25685]	5599.85	5683	1.01485	
2621	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [source:swissprot;acc:p46055]	5599.85	5683	1.01485	
2622	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [source:refseq;acc:nm_022553]	5599.85	5683	1.01485	
2623	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [source:swissprot;acc:o00203]	6815.24	6916.14	1.01481	
2624	ny-ren-24 antigen (fragment). [source:sptrembl;acc:q9y5a4]	6815.24	6916.14	1.01481	
2625	adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [source:swissprot;acc:q13367]	6815.24	6916.14	1.01481	
2626	insulin gene enhancer protein isl-1 (islet-1). [source:swissprot;acc:p20663]	7424.26	7534.05	1.01479	

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/