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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2125 to 2174 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
266	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Rooted	Divided	66.1064	74.1074	1.12103	
266	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Ranked	Subtracted	243.12	266.662	23.542	
266	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	Measured	Subtracted	11222.2	9948.93	1273.27	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Ranked	Divided	241.07	267.88	1.11121	
267	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Ranked	Subtracted	243.12	266.661	23.541	
267	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	Measured	Subtracted	11222.2	9948.93	1273.27	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Ranked	Divided	241.07	267.88	1.11121	
267	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	Squared	Subtracted	59334.6	68040.1	8705.5	
267	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Squared	Divided	26157.6	20236.2	1.29261	
267	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Measured	Divided	14021.4	11523	1.21682	
267	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Rooted	Subtracted	61.2893	70.3856	9.0963	
267	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Rooted	Divided	66.1064	74.1073	1.12103	
268	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	Measured	Subtracted	11222.2	9948.93	1273.27	
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Measured	Divided	24473.9	20127.8	1.21593	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Ranked	Divided	271.016	244.167	1.10996	
268	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Squared	Divided	26157.6	20236.2	1.29261	
268	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Rooted	Subtracted	61.2893	70.3856	9.0963	
268	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Ranked	Subtracted	241.625	265.136	23.511	
268	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Rooted	Divided	66.1064	74.1074	1.12103	
268	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	Squared	Subtracted	35533.9	44227	8693.1	
269	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Ranked	Subtracted	241.625	265.136	23.511	
269	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	Squared	Subtracted	35508.7	44191.4	8682.7	
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Ranked	Divided	241.373	267.352	1.10763	
269	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Measured	Subtracted	4808.79	6074.21	1265.42	
269	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]	Rooted	Subtracted	61.2893	70.3856	9.0963	
269	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Squared	Divided	26157.6	20236.2	1.29261	
269	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Rooted	Divided	66.1064	74.1074	1.12103	
269	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Measured	Divided	4590.18	5575.52	1.21466	
270	40s ribosomal protein s3. [source:swissprot;acc:p23396]	Ranked	Subtracted	241.612	265.119	23.507	
270	crk-like protein. [source:swissprot;acc:p46109]	Rooted	Divided	66.1064	74.1074	1.12103	
270	fad synthetase. [source:refseq;acc:nm_025207]	Ranked	Divided	241.373	267.352	1.10763	
270	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Measured	Divided	23640.2	19479.8	1.21358	
270	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	Squared	Subtracted	35508.6	44191.3	8682.7	
270	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Measured	Subtracted	4810.22	6075.04	1264.82	
270	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Rooted	Subtracted	48.0515	39.0445	9.007	
270	transcription factor iib. [source:refseq;acc:nm_013242]	Squared	Divided	64739.9	50300.6	1.28706	
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Ranked	Divided	241.373	267.352	1.10763	
271	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Measured	Divided	2554.89	3093.78	1.21092	
271	coatomer beta subunit (beta-coat protein) (beta-cop). [source:swissprot;acc:p53618]	Squared	Subtracted	53774.6	45105.5	8669.1	
271	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Rooted	Subtracted	62.762	53.7761	8.9859	
271	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Measured	Subtracted	4812.01	6076.09	1264.08	
271	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	Ranked	Subtracted	243.072	266.559	23.487	
271	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Rooted	Divided	66.1064	74.1073	1.12103	
271	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	Squared	Divided	64739.9	50300.6	1.28706	
272	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Squared	Divided	36563.7	46971.1	1.28464	
272	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Rooted	Subtracted	57.4432	66.3307	8.8875	
272	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Measured	Divided	3858.52	4669.27	1.21012	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Ranked	Divided	241.373	267.352	1.10763	
272	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	Ranked	Subtracted	242.83	266.248	23.418	
272	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Measured	Subtracted	1991.03	3221.38	1230.35	

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/