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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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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 662 to 711 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
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	
693	NOVA1	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]	222.554	234.847	1.05524	
694	POLE	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [source:swissprot;acc:q07864]	241.907	229.35	1.05475	
695	PPIL4	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [source:refseq;acc:nm_139126]	226.135	214.405	1.05471	
696	SFRS18	sr rich protein. [source:refseq;acc:nm_032870]	225.293	213.64	1.05455	
697	FTH1	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	220.444	209.113	1.05419	
698	FTMT	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	220.437	209.118	1.05413	
699	CREG2	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	220.438	209.118	1.05413	
700		dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	220.438	209.118	1.05413	
701	DLGAP1	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	220.438	209.118	1.05413	
702	AHCYL1	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	220.438	209.118	1.05413	
703	KIAA0430	limkain b1. [source:refseq;acc:nm_019081]	220.438	209.118	1.05413	
704		putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	220.438	209.118	1.05413	
705	CREG1	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	220.438	209.118	1.05413	
706	DLGAP3	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	220.438	209.118	1.05413	
707	KNG1	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	220.438	209.118	1.05413	
708		disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	220.438	209.118	1.05413	
709	FTL	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	220.438	209.118	1.05413	
710	DLGAP4	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	220.438	209.118	1.05413	
711	YARS	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [source:swissprot;acc:p54577]	232.468	245.048	1.05411	

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/