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 2858 to 2907 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1
red	0.00001
green	0.00001
network_comparison	1

Rank	Hugo	description	
2858	RYK	tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [source:swissprot;acc:p34925]	
2859	NKX6-1	homeobox protein nkx-6.1. [source:swissprot;acc:p78426]	
2860		importin 9. [source:refseq;acc:nm_018085]	
2861	GNPDA2	glucosamine-6-phosphate isomerase. [source:refseq;acc:nm_138335]	
2862	SDC3	syndecan-3 (synd3). [source:swissprot;acc:o75056]	
2863		high-glucose-regulated protein 8 (ny-ren-2 antigen). [source:swissprot;acc:q9y5a9]	
2864	MAGOH	mago nashi protein homolog. [source:swissprot;acc:p50606]	
2865	TAL1	t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [source:swissprot;acc:p17542]	
2866	STX5	syntaxin 5. [source:swissprot;acc:q13190]	
2867		sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [source:swissprot;acc:q9nzq3]	
2868	SNORA67	eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [source:swissprot;acc:p04765]	
2869	PRPSAP1	phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [source:swissprot;acc:q14558]	
2870	SH2B2	adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm_020979]	
2871	VPS28	vps28 protein homolog. [source:swissprot;acc:q9uk41]	
2872	BTBD14B	transcriptional repressor nac1. [source:refseq;acc:nm_052876]	
2873	ITGB2	integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [source:swissprot;acc:p05107]	
2874	C21orf2	protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [source:swissprot;acc:o43822]	
2875	CRYAA	alpha crystallin a chain. [source:swissprot;acc:p02489]	
2876	PDE9A	high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [source:swissprot;acc:o76083]	
2877	RUNX1	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [source:swissprot;acc:q01196]	
2878	NDUFS2	nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [source:swissprot;acc:o75306]	
2879		spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	
2880		microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	
2881	COLEC12	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [source:refseq;acc:nm_130386]	
2882	XDH	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [source:swissprot;acc:p47989]	
2883	PANK4	pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [source:swissprot;acc:q9nve7]	
2884	PDF	peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [source:swissprot;acc:q9hbh1]	
2885	CPT2	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]	
2886	C8A	complement component c8 alpha chain precursor. [source:swissprot;acc:p07357]	
2887	ZFYVE9	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [source:swissprot;acc:o95405]	
2888	EIF4A2	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [source:swissprot;acc:q14240]	
2889	UGT2B4	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]	
2890	CNOT8	ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [source:swissprot;acc:q9uff9]	
2891	SLC25A28	putative mitochondrial solute carrier; hypothetical protein npd016; putative mitochondrial solute carrier. [source:refseq;acc:nm_031212]	
2892	CDC2L6	cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [source:refseq;acc:nm_015076]	
2893	ATP5J	atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]	
2894	GTF2E1	transcription initiation factor iie, alpha subunit (tfiie-alpha) (general transcription factor iie 56 kda subunit). [source:swissprot;acc:p29083]	
2895		ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [source:swissprot;acc:p21108]	
2896	BMP6	bone morphogenetic protein 6 precursor (bmp-6). [source:swissprot;acc:p22004]	
2897		serine/threonine kinase 38 like. [source:refseq;acc:nm_015000]	
2898	CLEC4F	likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [source:refseq;acc:nm_173535]	
2899	SPARCL1	sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [source:swissprot;acc:q14515]	
2900	SCHIP1	schwannomin interacting protein 1. [source:refseq;acc:nm_014575]	
2901	CSNK1G3	casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [source:swissprot;acc:q9y6m4]	
2902	UBE3B	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	
2903	SEC24D	protein transport protein sec24d (sec24-related protein d). [source:swissprot;acc:o94855]	
2904	PTS	6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]	
2905	ITGB1	integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [source:swissprot;acc:p05556]	
2906	TAOK2	thousand and one amino acid protein kinase. [source:refseq;acc:nm_004783]	
2907	ALDOA	fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [source:swissprot;acc:p04075]	

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/