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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 643 to 692 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
643	HRBL	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [source:refseq;acc:nm_006076]	217.67	230.596	1.05938	
644	C16orf35	cgthba protein (-14 gene protein). [source:swissprot;acc:q12980]	217.67	230.596	1.05938	
645	HTATSF1	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [source:refseq;acc:nm_014500]	217.67	230.596	1.05938	
646	SCOC	short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm_032547]	216.731	229.549	1.05914	
647	DYNLL2	dynein light chain 2. [source:refseq;acc:nm_080677]	216.731	229.549	1.05914	
648	MARS	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	218.227	206.078	1.05895	
649	EIF4E	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	233.725	220.751	1.05877	
650		u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	228.986	216.276	1.05877	
651	BAIAP3	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	233.725	220.751	1.05877	
652		tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	248.994	235.255	1.0584	
653		dok-like protein. [source:refseq;acc:nm_024872]	216.504	204.622	1.05807	
654	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	216.504	204.622	1.05807	
655	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	216.504	204.622	1.05807	
656	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	216.504	204.622	1.05807	
657	SYN3	synapsin iii. [source:swissprot;acc:o14994]	229.072	216.576	1.0577	
658		aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	229.072	216.576	1.0577	
659	HEY1	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]	229.072	216.576	1.0577	
660	ABLIM2	actin binding lim protein 2. [source:refseq;acc:nm_032432]	229.072	216.576	1.0577	
661	HEYL	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	229.072	216.576	1.0577	
662	SYN2	synapsin ii. [source:swissprot;acc:q92777]	229.072	216.576	1.0577	
663	MRRF	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	229.072	216.576	1.0577	
664	PEX5	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	229.072	216.576	1.0577	
665	HEY2	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	229.072	216.576	1.0577	
666	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	229.072	216.576	1.0577	
667	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	229.072	216.576	1.0577	
668	ABLIM1	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	229.072	216.576	1.0577	
669	SYN1	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	229.072	216.576	1.0577	
670	GNL2	autoantigen ngp-1. [source:swissprot;acc:q13823]	250.302	236.817	1.05694	
671	NUBP1	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	210.739	199.398	1.05688	
672	NUBP2	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	210.739	199.398	1.05688	
673	CASK	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	226.497	214.355	1.05664	
674	HIF3A	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	226.497	214.355	1.05664	
675	SIM1	single-minded homolog 1. [source:swissprot;acc:p81133]	226.497	214.355	1.05664	
676	POLR2G	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	232.469	245.613	1.05654	
677	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	228.944	216.745	1.05628	
678	SNX5	sorting nexin 5. [source:swissprot;acc:q9y5x3]	208.482	220.175	1.05609	
679		homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	132.413	125.389	1.05602	
680	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	132.413	125.389	1.05602	
681	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	132.413	125.389	1.05602	
682		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	132.413	125.389	1.05602	
683	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	132.413	125.389	1.05602	
684	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	132.413	125.389	1.05602	
685	HOXA5	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	132.413	125.389	1.05602	
686		homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	132.413	125.389	1.05602	
687	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	132.413	125.389	1.05602	
688	POLR2D	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	237.554	250.823	1.05586	
689	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	135.379	128.225	1.05579	
690	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	220.593	208.987	1.05553	
691	BCAS2	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm_005872]	217.602	206.195	1.05532	
692	CDC5L	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [source:refseq;acc:nm_001253]	217.602	206.195	1.05532	

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/