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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 244 to 293 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
244	GSTO2	ba127l20.1 (novel glutathione-s-transferase). [source:sptrembl;acc:q9h4y5]	227.357	254.15	1.11785	
245	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	226.109	202.333	1.11751	
246	EIF4G3	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	237.312	212.363	1.11748	
247		rna-binding protein. [source:refseq;acc:nm_019027]	237.302	212.41	1.11719	
248		apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	237.302	212.41	1.11719	
249	SYNCRIP	ns1-associated protein 1. [source:refseq;acc:nm_006372]	237.302	212.41	1.11719	
250	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	237.302	212.41	1.11719	
251	SLC15A1	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	186.172	166.661	1.11707	
252	EIF4G1	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	237.292	212.457	1.11689	
253	MXD1	mad protein (max dimerizer). [source:swissprot;acc:q05195]	228	204.333	1.11583	
254	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	200.691	179.88	1.11569	
255	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	200.691	179.88	1.11569	
256	MXI1	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	227.999	204.357	1.11569	
257	DDOST	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]	200.691	179.88	1.11569	
258	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	227.999	204.366	1.11564	
259	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	227.999	204.37	1.11562	
260	HS3ST6	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	219.421	196.978	1.11394	
261	HS3ST3A1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	219.421	196.978	1.11394	
262	HS3ST3B1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	219.421	196.978	1.11394	
263	HS3ST2	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	219.421	196.978	1.11394	
264	DCPS	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	219.421	196.978	1.11394	
265	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	225.217	202.459	1.11241	
266	SIN3A	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	241.07	267.88	1.11121	
267	DENR	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	241.07	267.88	1.11121	
268	EIF5	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	271.016	244.167	1.10996	
269	PCYT1A	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]	241.373	267.352	1.10763	
270	FLAD1	fad synthetase. [source:refseq;acc:nm_025207]	241.373	267.352	1.10763	
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]	241.373	267.352	1.10763	
272	LGTN	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	241.373	267.352	1.10763	
273	PAPSS1	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]	241.373	267.352	1.10763	
274	POR	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	241.373	267.352	1.10763	
275	PCYT1B	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]	241.373	267.352	1.10763	
276	SNORA7A	60s ribosomal protein l32. [source:swissprot;acc:p02433]	241.13	266.969	1.10716	
277		40s ribosomal protein s29. [source:swissprot;acc:p30054]	241.849	267.642	1.10665	
278	RPS11	40s ribosomal protein s11. [source:swissprot;acc:p04643]	241.399	267.088	1.10642	
279	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	252.644	228.42	1.10605	
280	MTA1	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	252.512	228.356	1.10578	
281		60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	241.808	267.335	1.10557	
282	RBBP4	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]	252.39	228.297	1.10553	
283	RPL11	60s ribosomal protein l11. [source:swissprot;acc:p39026]	241.828	267.346	1.10552	
284	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	224.657	203.235	1.10541	
285	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	224.647	203.242	1.10532	
286	NEDD9	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]	224.633	203.251	1.1052	
287	RPS4Y2	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	240.758	266.079	1.10517	
288		40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	240.758	266.078	1.10517	
289		hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	272.781	246.892	1.10486	
290	RRM2	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	231.969	210.064	1.10428	
291	NFYB	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]	251.679	228.037	1.10368	
292	RPS15A	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	241.411	266.414	1.10357	
293		60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	240.782	265.717	1.10356	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/