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 1901 to 1950 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
476	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [source:swissprot;acc:q15825]	Measured	9649.61	11053.5	1.14549	
476	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [source:swissprot;acc:p22459]	Ranked	226.681	210.814	1.07527	
476	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Rooted	62.574	68.4128	1.09331	
476	vav proto-oncogene. [source:swissprot;acc:p15498]	Squared	31223.8	37614.3	1.20467	
477	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Rooted	62.574	68.4128	1.09331	
477	nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	Measured	9649.61	11053.5	1.14549	
477	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Ranked	251.926	234.547	1.0741	
477	vav-3 protein. [source:swissprot;acc:q9ukw4]	Squared	31248.8	37623.4	1.204	
478	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	Rooted	50.6084	55.2961	1.09263	
478	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Squared	16318.4	19645.8	1.2039	
478	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]	Measured	9649.61	11053.5	1.14549	
478	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	Ranked	228.051	212.321	1.07409	
479	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Rooted	50.6084	55.2961	1.09263	
479	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	Ranked	228.051	212.321	1.07409	
479	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]	Measured	9649.61	11053.5	1.14549	
479	translation initiation factor if-2. [source:swissprot;acc:o60841]	Squared	24031.6	28929.7	1.20382	
480	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Rooted	50.6084	55.2961	1.09263	
480	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]	Measured	9649.61	11053.5	1.14549	
480	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	Ranked	237.109	254.667	1.07405	
480	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	Squared	26874.6	32347.4	1.20364	
481	histone h2b. [source:refseq;acc:nm_175055]	Rooted	50.6084	55.2961	1.09263	
481	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm_004635]	Measured	9649.61	11053.5	1.14549	
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	Ranked	237.109	254.667	1.07405	
481	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Squared	16335.9	19660.7	1.20353	
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	Ranked	237.109	254.667	1.07405	
482	histone h2b.s (h2b/s). [source:swissprot;acc:p57053]	Rooted	50.6084	55.2961	1.09263	
482	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [source:swissprot;acc:q16539]	Measured	9649.61	11053.5	1.14549	
482	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [source:swissprot;acc:q8wwt9]	Squared	26867.3	32335.2	1.20352	
483	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	Rooted	50.6084	55.2961	1.09263	
483	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [source:swissprot;acc:p43681]	Measured	9649.61	11053.5	1.14549	
483	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	Ranked	237.109	254.667	1.07405	
483	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	Squared	26867.3	32335.2	1.20352	
484	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	Ranked	237.109	254.667	1.07405	
484	histone h3.4 (h3t) (h3/t) (h3/g). [source:swissprot;acc:q16695]	Rooted	50.6084	55.2961	1.09263	
484	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297]	Measured	9649.61	11053.5	1.14549	
484	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [source:swissprot;acc:q9ukg4]	Squared	26867.2	32335	1.20351	
485	60s ribosomal protein l18. [source:swissprot;acc:q07020]	Ranked	237.109	254.667	1.07405	
485	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	Squared	26867.2	32335	1.20351	
485	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	Measured	9649.61	11053.5	1.14549	
485	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [source:refseq;acc:nm_170610]	Rooted	50.6084	55.2961	1.09263	
486	histone h2b.e (h2b/e). [source:swissprot;acc:q99879]	Rooted	50.6084	55.2961	1.09263	
486	mct-1 protein. [source:refseq;acc:nm_014060]	Ranked	226.313	243.03	1.07387	
486	secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	Squared	26865.9	32332.9	1.20349	
486	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Measured	10908.6	12491.8	1.14513	
487	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	Ranked	226.313	243.03	1.07387	
487	pyrroline 5-carboxylate reductase isoform. [source:refseq;acc:nm_013328]	Measured	5277.4	6042.88	1.14505	
487	secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	Squared	26865.9	32332.9	1.20349	
487	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Rooted	50.0015	54.627	1.09251	
488	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Measured	10872.4	12447	1.14483	
488	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	Rooted	50.4315	46.1703	1.09229	

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/