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 2013 to 2062 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
252	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Ranked	Subtracted	228	204.333	23.667	
252	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	Rooted	Divided	51.6736	58.4422	1.13099	
252	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	Squared	Divided	69165	52991.7	1.3052	
252	sedlin. [source:swissprot;acc:o14582]	Rooted	Subtracted	116.061	125.434	9.373	
253	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	Squared	Divided	69165	52991.7	1.3052	
253	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	Measured	Subtracted	9642.22	10986.4	1344.18	
253	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	Squared	Subtracted	39478.8	48419	8940.2	
253	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Ranked	Divided	228	204.333	1.11583	
253	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	Ranked	Subtracted	251.679	228.037	23.642	
253	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Measured	Divided	6417.18	7859.59	1.22477	
253	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Rooted	Divided	53.5956	60.465	1.12817	
253	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Rooted	Subtracted	116.061	125.434	9.373	
254	bet3 homolog. [source:swissprot;acc:o43617]	Rooted	Subtracted	116.061	125.434	9.373	
254	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Measured	Subtracted	9634.98	10976.2	1341.22	
254	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Ranked	Subtracted	227.999	204.357	23.642	
254	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Measured	Divided	6417.18	7859.6	1.22477	
254	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Rooted	Divided	53.607	60.4452	1.12756	
254	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Ranked	Divided	200.691	179.88	1.11569	
254	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [source:swissprot;acc:o95718]	Squared	Subtracted	59338.5	68268.3	8929.8	
254	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	Squared	Divided	69165	52991.7	1.3052	
255	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	Squared	Divided	69123.3	52967	1.30503	
255	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	Squared	Subtracted	39472	48393.1	8921.1	
255	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Measured	Subtracted	4455.95	5774.03	1318.08	
255	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Ranked	Subtracted	227.999	204.366	23.633	
255	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Ranked	Divided	200.691	179.88	1.11569	
255	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Rooted	Subtracted	132.156	122.835	9.321	
255	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Measured	Divided	6417.18	7859.6	1.22477	
255	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Rooted	Divided	62.9007	70.8854	1.12694	
256	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [source:swissprot;acc:q03701]	Rooted	Divided	48.0045	54.0843	1.12665	
256	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Rooted	Subtracted	132.114	122.802	9.312	
256	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Squared	Divided	15465.1	20151	1.303	
256	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Squared	Subtracted	39463.9	48362.1	8898.2	
256	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]	Measured	Divided	6417.19	7859.51	1.22476	
256	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Ranked	Subtracted	227.999	204.37	23.629	
256	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Measured	Subtracted	4456.67	5773.77	1317.1	
256	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Ranked	Divided	227.999	204.357	1.11569	
257	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Rooted	Divided	51.6125	45.8409	1.12591	
257	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Measured	Divided	6417.31	7858.12	1.22452	
257	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Rooted	Subtracted	132.467	123.158	9.309	
257	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	Divided	200.691	179.88	1.11569	
257	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Squared	Divided	15482.3	20162.4	1.30229	
257	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Measured	Subtracted	4456.93	5773.67	1316.74	
257	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Squared	Subtracted	33526	42390.2	8864.2	
257	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	Ranked	Subtracted	242.14	265.697	23.557	
258	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	Ranked	Subtracted	242.14	265.697	23.557	
258	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Measured	Divided	6417.33	7857.93	1.22449	
258	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	Squared	Divided	76438	58889.7	1.29799	
258	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Measured	Subtracted	4457.06	5773.63	1316.57	
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Ranked	Divided	227.999	204.366	1.11564	
258	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Squared	Subtracted	33522.8	42384.8	8862	

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/