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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2025 to 2074 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
2025	GPT	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [source:swissprot;acc:p24298]	189.987	191.668	1.00885	
2026	VPS11	vacuolar protein sorting 11 (hvps11) (pp3476). [source:swissprot;acc:q9h270]	215.553	213.663	1.00885	
2027	LIN7C	lin-7 homolog c; lin-7 protein 3. [source:refseq;acc:nm_018362]	225.015	223.041	1.00885	
2028	VPS33A	vacuolar protein sorting 33a (hvps33a). [source:swissprot;acc:q96ax1]	215.553	213.663	1.00885	
2029	CCBL1	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [source:refseq;acc:nm_004059]	189.999	191.677	1.00883	
2030	GPT2	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [source:refseq;acc:nm_133443]	189.999	191.677	1.00883	
2031	TTRAP	traf and tnf receptor-associated protein; ets1-associated protein 2. [source:refseq;acc:nm_016614]	218.466	216.562	1.00879	
2032	CAPZA3	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [source:swissprot;acc:q96kx2]	215.322	213.46	1.00872	
2033	CAPZB	f-actin capping protein beta subunit (capz beta). [source:swissprot;acc:p47756]	215.322	213.46	1.00872	
2034	CENTB5	centaurin beta 5 (cnt-b5). [source:swissprot;acc:q96p50]	218.919	220.812	1.00865	
2035	CENTB2	centaurin beta 2 (cnt-b2). [source:swissprot;acc:q15057]	218.919	220.812	1.00865	
2036	LMNB1	lamin b1. [source:swissprot;acc:p20700]	218.919	220.813	1.00865	
2037	CENTB1	centaurin beta 1 (cnt-b1). [source:swissprot;acc:q15027]	218.919	220.812	1.00865	
2038	LMNA	lamin a/c (70 kda lamin). [source:swissprot;acc:p02545]	218.92	220.811	1.00864	
2039	ACSS2	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [source:swissprot;acc:q9nr19]	190.551	192.191	1.00861	
2040	T	brachyury protein (t protein). [source:swissprot;acc:o15178]	210.586	208.803	1.00854	
2041	UBQLN4	ataxin-1 ubiquitin-like interacting protein. [source:refseq;acc:nm_020131]	196.808	195.141	1.00854	
2042	TBX19	t-box transcription factor tbx19 (t-box protein 19). [source:swissprot;acc:o60806]	210.586	208.803	1.00854	
2043	UBQLN1	ubiquilin 1 isoform 1. [source:refseq;acc:nm_013438]	196.837	195.173	1.00853	
2044	AP3B1	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [source:swissprot;acc:o00203]	199.928	198.24	1.00851	
2045	C19orf29	ny-ren-24 antigen (fragment). [source:sptrembl;acc:q9y5a4]	199.928	198.24	1.00851	
2046		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]	199.928	198.24	1.00851	
2047	SLC2A6	solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [source:swissprot;acc:q9ugq3]	224.124	226.003	1.00838	
2048	SLC2A8	solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [source:swissprot;acc:q9ny64]	224.124	226.003	1.00838	
2049	EIF2B2	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [source:swissprot;acc:p49770]	220.787	222.634	1.00837	
2050	SH3BGR	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [source:swissprot;acc:p55822]	218.79	216.981	1.00834	
2051	OXR1	oxidation resistance 1. [source:refseq;acc:nm_181354]	218.79	216.981	1.00834	
2052	AZIN1	ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	207.667	205.95	1.00834	
2053	LATS2	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [source:refseq;acc:nm_014572]	218.79	216.981	1.00834	
2054	ADC	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	207.665	205.948	1.00834	
2055	DYM	dymeclin. [source:refseq;acc:nm_017653]	218.79	216.981	1.00834	
2056	SH3BGRL	sh3 domain-binding glutamic acid-rich-like protein. [source:swissprot;acc:o75368]	218.79	216.981	1.00834	
2057	LATS1	lats homolog 1. [source:refseq;acc:nm_004690]	218.79	216.981	1.00834	
2058		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [source:swissprot;acc:q9ujc5]	218.79	216.981	1.00834	
2059	NCOA7	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [source:refseq;acc:nm_181782]	218.79	216.981	1.00834	
2060	C20orf118	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [source:sptrembl;acc:q9h125]	218.79	216.981	1.00834	
2061	TBC1D22B	tbc1 domain family protein c22orf4-like (fragment). [source:swissprot;acc:q9nu19]	218.79	216.981	1.00834	
2062	TBC1D22A	tbc1 domain family protein c22orf4. [source:swissprot;acc:q8wua7]	218.79	216.981	1.00834	
2063	ODC1	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	207.638	205.923	1.00833	
2064	AASS	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	207.655	205.939	1.00833	
2065	UBE2N	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [source:swissprot;acc:q16781]	214.328	212.561	1.00831	
2066	PCNA	proliferating cell nuclear antigen (pcna) (cyclin). [source:swissprot;acc:p12004]	229.102	231.001	1.00829	
2067	ADSL	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [source:swissprot;acc:p30566]	193.226	191.639	1.00828	
2068	FAIM	fas apoptotic inhibitory molecule. [source:refseq;acc:nm_018147]	220.8	222.61	1.0082	
2069	MAP2K1	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [source:swissprot;acc:q02750]	217.555	215.807	1.0081	
2070	RACGAP1	rac gtpase activating protein 1; gtpase activating protein. [source:refseq;acc:nm_013277]	223.199	225.008	1.0081	
2071	KSR1	similar to kinase suppressor of ras (fragment). [source:sptrembl;acc:q8ivt5]	217.555	215.807	1.0081	
2072	MAP2K2	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [source:swissprot;acc:p36507]	217.555	215.807	1.0081	
2073	PAPD5	topoisomerase-related function protein 4-2. [source:refseq;acc:nm_022447]	229.267	227.433	1.00806	
2074	POLG	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [source:swissprot;acc:p54098]	216.324	214.599	1.00804	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/