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 1618 to 1667 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
1618	TCEA2	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [source:swissprot;acc:q15560]	227.768	231.246	1.01527	
1619		transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	227.768	231.246	1.01527	
1620	GTF2B	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [source:swissprot;acc:q00403]	228.611	225.185	1.01521	
1621	ZNHIT3	thyroid receptor interacting protein 3 (trip-3) (fragment). [source:swissprot;acc:q15649]	228.611	225.185	1.01521	
1622	NHP2L1	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [source:swissprot;acc:p55769]	228.611	225.185	1.01521	
1623	NUFIP1	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [source:refseq;acc:nm_012345]	228.611	225.185	1.01521	
1624	PDCD11	rrp5 protein homolog (programmed cell death protein 11). [source:swissprot;acc:q14690]	230.643	227.194	1.01518	
1625	RPUSD2	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	217.446	214.2	1.01515	
1626	TMBIM4	z-protein (protein cgi-119) (s1r protein). [source:swissprot;acc:q9hc24]	217.446	214.2	1.01515	
1627	TMBIM1	pp1201 protein. [source:refseq;acc:nm_022152]	217.446	214.2	1.01515	
1628	FAIM2	lifeguard; kiaa0950 protein. [source:refseq;acc:nm_012306]	217.446	214.2	1.01515	
1629		sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	217.446	214.2	1.01515	
1630	SREBF1	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [source:swissprot;acc:p36956]	217.446	214.2	1.01515	
1631	GSPT1	g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [source:swissprot;acc:p15170]	218.789	215.533	1.01511	
1632	BUB3	mitotic checkpoint protein bub3. [source:swissprot;acc:o43684]	221.934	218.658	1.01498	
1633	ZNF207	zinc finger protein 207. [source:swissprot;acc:o43670]	221.934	218.658	1.01498	
1634	MLYCD	malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [source:swissprot;acc:o95822]	215.772	212.596	1.01494	
1635	ITCH	itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [source:refseq;acc:nm_031483]	215.772	212.596	1.01494	
1636	BECN1	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [source:swissprot;acc:q14457]	202.358	199.408	1.01479	
1637	PSMC5	26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [source:swissprot;acc:p47210]	202.358	199.408	1.01479	
1638	SHMT2	serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34897]	220.686	217.481	1.01474	
1639	VPS72	yl-1 protein (transcription factor-like 1). [source:swissprot;acc:q15906]	194.516	197.364	1.01464	
1640	HAGH	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [source:swissprot;acc:q16775]	194.516	197.364	1.01464	
1641	PSMB4	proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [source:swissprot;acc:p28070]	218.167	215.034	1.01457	
1642	CDC25B	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [source:swissprot;acc:p30305]	260.269	256.531	1.01457	
1643	PNKD	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [source:refseq;acc:nm_022572]	194.476	197.305	1.01455	
1644		secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	217.256	214.149	1.01451	
1645	PFDN1	prefoldin subunit 1. [source:swissprot;acc:o60925]	217.256	214.149	1.01451	
1646	SMOC2	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [source:refseq;acc:nm_022138]	217.256	214.149	1.01451	
1647	CHDH	choline dehydrogenase. [source:refseq;acc:nm_018397]	217.256	214.149	1.01451	
1648		hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [source:swissprot;acc:p46597]	219.745	222.928	1.01448	
1649	PRSS12	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [source:swissprot;acc:p56730]	219.062	215.942	1.01445	
1650	RNF44	ring finger protein 44. [source:refseq;acc:nm_014901]	219.062	215.942	1.01445	
1651	PIK3R1	phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [source:swissprot;acc:p27986]	219.062	215.942	1.01445	
1652	RNF38	ring finger protein 38. [source:refseq;acc:nm_022781]	219.062	215.942	1.01445	
1653	PIK3R3	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [source:swissprot;acc:q92569]	219.062	215.942	1.01445	
1654	SCAP	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [source:swissprot;acc:q12770]	219.062	215.942	1.01445	
1655	ATP5B	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p06576]	219.062	215.942	1.01445	
1656	PIK3R2	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [source:swissprot;acc:o00459]	219.062	215.942	1.01445	
1657	NUDT21	cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [source:refseq;acc:nm_007006]	219.314	216.195	1.01443	
1658	ATP5A1	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	217.925	214.826	1.01443	
1659	MRPS18A	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	217.925	214.826	1.01443	
1660	EEA1	early endosome antigen 1, 162kd; early endosome-associated protein. [source:refseq;acc:nm_003566]	228.654	231.933	1.01434	
1661	ADSSL1	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	204.437	201.551	1.01432	
1662	MORF4L2	transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [source:swissprot;acc:q15014]	228.477	231.747	1.01431	
1663	TDO2	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [source:swissprot;acc:p48775]	218.335	215.26	1.01429	
1664		transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [source:swissprot;acc:q9y690]	228.484	231.74	1.01425	
1665	ADSS	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source:swissprot;acc:p30520]	204.433	201.564	1.01423	
1666	TNPO2	karyopherin beta 2b, transportin; importin 3. [source:refseq;acc:nm_013433]	218.679	215.612	1.01422	
1667	CTSB	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [source:swissprot;acc:p07858]	214.898	211.898	1.01416	

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/