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 1051 to 1100 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
263	paxillin. [source:swissprot;acc:p49023]	Rooted	59.4073	66.7002	1.12276	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	Measured	24896.4	20431.7	1.21852	
264	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Squared	26157.6	20236.2	1.29261	
264	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Measured	4987.58	4094.57	1.2181	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Ranked	219.421	196.978	1.11394	
264	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Rooted	66.1122	74.1438	1.12148	
265	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Squared	26157.6	20236.2	1.29261	
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Ranked	225.217	202.459	1.11241	
265	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Rooted	56.031	62.8281	1.12131	
265	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Measured	24806.9	20369.9	1.21782	
266	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Measured	24806.9	20369.9	1.21782	
266	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Squared	26157.6	20236.2	1.29261	
266	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Rooted	66.1064	74.1074	1.12103	
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Ranked	241.07	267.88	1.11121	
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Ranked	241.07	267.88	1.11121	
267	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Squared	26157.6	20236.2	1.29261	
267	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Measured	14021.4	11523	1.21682	
267	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Rooted	66.1064	74.1073	1.12103	
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Measured	24473.9	20127.8	1.21593	
268	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Ranked	271.016	244.167	1.10996	
268	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Squared	26157.6	20236.2	1.29261	
268	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Rooted	66.1064	74.1074	1.12103	
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	241.373	267.352	1.10763	
269	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Squared	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	66.1064	74.1074	1.12103	
269	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Measured	4590.18	5575.52	1.21466	
270	crk-like protein. [source:swissprot;acc:p46109]	Rooted	66.1064	74.1074	1.12103	
270	fad synthetase. [source:refseq;acc:nm_025207]	Ranked	241.373	267.352	1.10763	
270	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Measured	23640.2	19479.8	1.21358	
270	transcription factor iib. [source:refseq;acc:nm_013242]	Squared	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	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	2554.89	3093.78	1.21092	
271	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Rooted	66.1064	74.1073	1.12103	
271	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	Squared	64739.9	50300.6	1.28706	
272	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Squared	36563.7	46971.1	1.28464	
272	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Measured	3858.52	4669.27	1.21012	
272	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Ranked	241.373	267.352	1.10763	
272	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Rooted	66.1064	74.1074	1.12103	
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252]	Ranked	241.373	267.352	1.10763	
273	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Measured	3199.4	3870.8	1.20985	
273	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Squared	16120.1	20665.7	1.28198	
273	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Rooted	66.1064	74.1074	1.12103	
274	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Measured	3119.98	2579.49	1.20953	
274	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	Rooted	66.1063	74.1068	1.12102	
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Ranked	241.373	267.352	1.10763	
274	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Squared	16120.1	20665.7	1.28198	
275	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Rooted	66.1048	74.0977	1.12091	
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Ranked	241.373	267.352	1.10763	
275	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Squared	16120.1	20665.7	1.28198	
275	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	Measured	3119.98	2579.49	1.20953	

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/