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 1077 to 1126 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
539	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	Subtracted	112	126	14	
539	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	Divided	236.964	252.86	1.06708	
540	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Subtracted	58	44	14	
540	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Divided	222.156	208.201	1.06703	
541	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Divided	222.156	208.201	1.06703	
541	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Subtracted	112	126	14	
542	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Divided	222.156	208.201	1.06703	
542	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Subtracted	112	126	14	
543	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Subtracted	112	126	14	
543	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Divided	222.156	208.201	1.06703	
544	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Subtracted	112	126	14	
544	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Divided	222.156	208.201	1.06703	
545	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Divided	248.866	233.287	1.06678	
545	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Subtracted	58	44	14	
546	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Subtracted	112	126	14	
546	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Divided	207.222	194.262	1.06671	
547	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	Subtracted	234.106	248.104	13.998	
547	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Divided	207.26	194.346	1.06645	
548	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Subtracted	222.156	208.201	13.955	
548	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Divided	207.26	194.346	1.06645	
549	flavoprotein oxidoreductase mical2. [source:refseq;acc:nm_014632]	Subtracted	222.156	208.201	13.955	
549	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Divided	207.26	194.346	1.06645	
550	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [source:refseq;acc:nm_003866]	Subtracted	222.156	208.201	13.955	
550	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Divided	207.26	194.346	1.06645	
551	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	Divided	207.261	194.347	1.06645	
551	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Subtracted	222.156	208.201	13.955	
552	crk-like protein. [source:swissprot;acc:p46109]	Divided	207.26	194.346	1.06645	
552	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Subtracted	222.156	208.201	13.955	
553	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Divided	207.26	194.346	1.06645	
553	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	Subtracted	226.3	212.38	13.92	
554	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Divided	207.26	194.346	1.06645	
554	t54 protein. [source:swissprot;acc:q92917]	Subtracted	226.3	212.38	13.92	
555	cbf1 interacting corepressor. [source:refseq;acc:nm_004882]	Subtracted	227.86	213.945	13.915	
555	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Divided	207.26	194.346	1.06645	
556	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Divided	207.27	194.368	1.06638	
556	evolutionarily conserved g-patch domain containing. [source:refseq;acc:nm_018025]	Subtracted	227.86	213.945	13.915	
557	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Divided	207.272	194.371	1.06637	
557	shwachman-bodian-diamond syndrome protein (cgi-97). [source:swissprot;acc:q9y3a5]	Subtracted	216.557	230.362	13.805	
558	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Subtracted	248.994	235.255	13.739	
558	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Divided	135.087	144.041	1.06628	
559	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Divided	207.309	194.452	1.06612	
559	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [source:swissprot;acc:p78346]	Subtracted	216.72	230.439	13.719	
560	son of sevenless protein homolog 1 (sos-1). [source:swissprot;acc:q07889]	Divided	205.74	193.021	1.06589	
560	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	Subtracted	232.118	218.406	13.712	
561	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	Divided	205.89	193.183	1.06578	
561	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Subtracted	228.215	214.546	13.669	
562	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Subtracted	224.606	210.944	13.662	
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Divided	220.744	207.121	1.06577	
563	calcyphosine. [source:swissprot;acc:q13938]	Divided	220.744	207.121	1.06577	
563	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	Subtracted	224.606	210.944	13.662	

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/