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 Interaction Map Network Comparison Type Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2601 to 2650 of 14920 in total 
    Interaction Map	High confidence
    Network Comparison Type	Divided
    
Rank	description	Value Type	Filtered	red	green	network_comparison	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	Ranked	1	241.899	265.924	1.09932	
326	anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [source:refseq;acc:nm_013366]	Squared	1	69124.3	54897.4	1.25915	
326	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	Rooted	0	83.9673	88.8829	1.05854	
326	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Measured	1	3432.96	4081.21	1.18883	
326	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	Measured	0	3053.31	2799.81	1.09054	
326	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	Ranked	0	11948.4	11295.6	1.05779	
326	germ cell-less. [source:refseq;acc:nm_022471]	Squared	0	3567.33	3084.18	1.15665	
326	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Rooted	1	50.3803	45.4193	1.10923	
327	3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Ranked	0	9897.29	10466.5	1.05751	
327	actin, cytoplasmic 2 (gamma-actin). [source:swissprot;acc:p02571]	Squared	0	178.482	205.335	1.15045	
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	1	50.3803	45.4193	1.10923	
327	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Measured	0	175.644	161.091	1.09034	
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	Ranked	1	243.817	267.962	1.09903	
327	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Squared	1	16424.1	20645.8	1.25704	
327	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [source:swissprot;acc:o95544]	Rooted	0	23.6959	25.0734	1.05813	
327	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Measured	1	16067.4	19094.4	1.18839	
328	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Squared	0	6747.71	5878.56	1.14785	
328	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Measured	0	1657.78	1805.05	1.08884	
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	Ranked	1	258.437	235.183	1.09888	
328	brain protein 44. [source:swissprot;acc:o95563]	Measured	1	15999.1	19007.1	1.18801	
328	histone h4. [source:swissprot;acc:p02304]	Rooted	0	98.5525	104.126	1.05655	
328	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Squared	1	16442.8	20662.7	1.25664	
328	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Rooted	1	50.3803	45.4193	1.10923	
328	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	Ranked	0	10897	11520	1.05717	
329	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	Squared	0	195397	170319	1.14724	
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	1	50.3803	45.4193	1.10923	
329	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	Measured	0	1658.07	1805.36	1.08883	
329	metaxin 2. [source:swissprot;acc:o75431]	Squared	1	41236	51807	1.25635	
329	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	Ranked	1	312	284	1.09859	
329	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Measured	1	15999.1	19007.1	1.18801	
329	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	Ranked	0	15977.3	15115.5	1.05701	
329	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [source:swissprot;acc:q16514]	Rooted	0	15.4404	16.3116	1.05642	
330	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Measured	0	1658.23	1805.52	1.08882	
330	60s ribosomal protein l32. [source:swissprot;acc:p02433]	Rooted	1	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	1	312	284	1.09859	
330	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Rooted	0	57.5016	60.7262	1.05608	
330	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	Squared	0	2758.07	3161.7	1.14635	
330	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Squared	1	16203.4	20339.9	1.25529	
330	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm_032152]	Ranked	0	12320.2	13018.5	1.05668	
330	septin 6. [source:swissprot;acc:q14141]	Measured	1	15959.9	18957.1	1.1878	
331	40s ribosomal protein s3a. [source:swissprot;acc:p49241]	Ranked	0	10405.1	10992.4	1.05644	
331	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Squared	0	26.2121	22.8932	1.14497	
331	alpha-nac protein. [source:sptrembl;acc:q9h009]	Rooted	0	9.95878	9.44328	1.05459	
331	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Rooted	1	60.6697	67.2802	1.10896	
331	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	Ranked	1	312	284	1.09859	
331	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	Measured	0	4088	4451	1.0888	
331	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Measured	1	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	1	33100.3	41520.6	1.25439	
332	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [source:swissprot;acc:q9nyg5]	Measured	0	15411.3	14167	1.08783	
332	basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	Rooted	0	15.297	14.5086	1.05434	

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/