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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2700 to 2749 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
338	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Measured	Subtracted	1631.67	2664.55	1032.88	
338	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Rooted	Divided	77.58	70.0181	1.108	
338	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Rooted	Subtracted	52.7557	60.035	7.2793	
338	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Ranked	Subtracted	200.691	179.88	20.811	
338	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [source:swissprot;acc:p15822]	Squared	Divided	46785.7	58383.2	1.24789	
339	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [source:swissprot;acc:q09028]	Rooted	Subtracted	52.7936	60.0592	7.2656	
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	Ranked	Divided	243.583	267.527	1.0983	
339	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Ranked	Subtracted	200.691	179.88	20.811	
339	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Measured	Divided	20446.1	24136.4	1.18049	
339	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	Squared	Divided	46785.7	58383.2	1.24789	
339	neuralized-like. [source:refseq;acc:nm_004210]	Measured	Subtracted	1657.68	2690.25	1032.57	
339	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Rooted	Divided	77.5797	70.0179	1.108	
339	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	Squared	Subtracted	28895.6	35572.8	6677.2	
340	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	Ranked	Subtracted	239.75	260.544	20.794	
340	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Measured	Divided	20446.1	24136.4	1.18049	
340	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	Ranked	Divided	235.383	258.476	1.09811	
340	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Rooted	Divided	58.4926	64.8047	1.10791	
340	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Squared	Divided	32117	40054	1.24713	
340	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [source:refseq;acc:nm_005843]	Measured	Subtracted	11743.3	10712.3	1031	
340	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Rooted	Subtracted	45.7414	52.932	7.1906	
340	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Squared	Subtracted	28895.6	35572.8	6677.2	
341	60s ribosomal protein l9. [source:swissprot;acc:p32969]	Ranked	Divided	240.243	263.798	1.09805	
341	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:o00763]	Squared	Subtracted	31646.1	38288.7	6642.6	
341	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Measured	Divided	20446.1	24136.4	1.18049	
341	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Rooted	Divided	51.9812	57.5858	1.10782	
341	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Rooted	Subtracted	120.033	112.905	7.128	
341	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Squared	Divided	32056.4	39965.8	1.24673	
341	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Measured	Subtracted	4916.8	3888.18	1028.62	
341	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	Ranked	Subtracted	240.788	261.416	20.628	
342	40s ribosomal protein s20. [source:swissprot;acc:p17075]	Ranked	Divided	243.5	267.21	1.09737	
342	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	Ranked	Subtracted	240.913	261.45	20.537	
342	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	Squared	Divided	70830.5	56822	1.24653	
342	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Measured	Divided	20446.1	24136.4	1.18049	
342	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	Rooted	Divided	49.2715	54.5757	1.10765	
342	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [source:swissprot;acc:o00743]	Squared	Subtracted	31620.5	38250.7	6630.2	
342	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	Measured	Subtracted	10230.1	11256.2	1026.1	
342	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Rooted	Subtracted	46.0352	53.0192	6.984	
343	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Rooted	Divided	50.3169	45.4333	1.10749	
343	conserved oligomeric golgi complex component 7. [source:swissprot;acc:p83436]	Squared	Divided	70830.5	56822	1.24653	
343	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Measured	Divided	20446.1	24136.4	1.18049	
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Ranked	Divided	241.625	265.136	1.0973	
343	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Ranked	Subtracted	231.73	211.252	20.478	
343	sporulation-induced transcript 4-associated protein. [source:refseq;acc:nm_018312]	Squared	Subtracted	31620.5	38250.7	6630.2	
343	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Rooted	Subtracted	46.0352	53.0192	6.984	
343	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Measured	Subtracted	4991.48	6014.08	1022.6	
344	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Ranked	Divided	241.625	265.136	1.0973	
344	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:q13085]	Squared	Subtracted	31597.8	38216.9	6619.1	
344	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Rooted	Subtracted	57.9068	64.8562	6.9494	
344	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	Measured	Subtracted	9921.43	10941.2	1019.77	
344	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	Ranked	Subtracted	240.6	261.041	20.441	

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/