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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 558 to 607 of 6456 in total 
    Value Type	Ranked
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
279	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Divided	252.644	228.42	1.10605	
280	MTA1	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Divided	252.512	228.356	1.10578	
280	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Subtracted	267.208	244.168	23.04	
281		60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Divided	241.808	267.335	1.10557	
281	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	Subtracted	242.159	265.104	22.945	
282	NUDT12	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Subtracted	242.159	265.104	22.945	
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]	Divided	252.39	228.297	1.10553	
283	MRPL11	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Subtracted	242.37	265.255	22.885	
283	RPL11	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Divided	241.828	267.346	1.10552	
284	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Divided	224.657	203.235	1.10541	
284	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	Subtracted	242.686	265.516	22.83	
285	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Divided	224.647	203.242	1.10532	
285	POLR1A	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	Subtracted	242.691	265.481	22.79	
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]	Divided	224.633	203.251	1.1052	
286	RPL30	60s ribosomal protein l30. [source:swissprot;acc:p04645]	Subtracted	242.593	265.365	22.772	
287	RPS4Y2	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Divided	240.758	266.079	1.10517	
287	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]	Subtracted	225.217	202.459	22.758	
288		40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Divided	240.758	266.078	1.10517	
288	STX10	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Subtracted	234.691	257.442	22.751	
289		hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Divided	272.781	246.892	1.10486	
289	STX6	syntaxin 6. [source:swissprot;acc:o43752]	Subtracted	234.673	257.414	22.741	
290		suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Subtracted	242.109	264.79	22.681	
290	RRM2	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Divided	231.969	210.064	1.10428	
291	AK2	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	Subtracted	241.509	264.163	22.654	
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]	Divided	251.679	228.037	1.10368	
292	HNRPM	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	Subtracted	234.146	256.627	22.481	
292	RPS15A	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	Divided	241.411	266.414	1.10357	
293		60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	Divided	240.782	265.717	1.10356	
293	HS3ST6	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Subtracted	219.421	196.978	22.443	
294	BCCIP	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [source:refseq;acc:nm_016567]	Divided	240.782	265.717	1.10356	
294	HS3ST3A1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Subtracted	219.421	196.978	22.443	
295	HS3ST3B1	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Subtracted	219.421	196.978	22.443	
295	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Divided	223.273	202.423	1.103	
296	HS3ST2	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Subtracted	219.421	196.978	22.443	
296	MRPL4	mitochondrial ribosomal protein l4 isoform a. [source:refseq;acc:nm_015956]	Divided	241.282	266.12	1.10294	
297		60s ribosomal protein l7. [source:swissprot;acc:p18124]	Divided	235.727	259.984	1.1029	
297	DCPS	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Subtracted	219.421	196.978	22.443	
298	CAPN2	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [source:swissprot;acc:p17655]	Divided	268.632	243.588	1.10281	
298	E2F1	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Subtracted	266.421	244.236	22.185	
299	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	Divided	268.635	243.592	1.10281	
299	E2F2	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Subtracted	266.421	244.236	22.185	
300	DDX56	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Subtracted	257.017	234.945	22.072	
300	PITRM1	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	Divided	150.959	166.351	1.10196	
301	ALG1	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Divided	150.982	166.372	1.10193	
301	MAGED4	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Subtracted	88.2482	110.265	22.0168	
302	MAGEE2	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Subtracted	88.2482	110.265	22.0168	
302	RPL26	60s ribosomal protein l26. [source:swissprot;acc:q02877]	Divided	242.326	267.008	1.10185	
303		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Subtracted	88.2482	110.265	22.0168	
303	RPL35	60s ribosomal protein l35. [source:swissprot;acc:p42766]	Divided	242.333	266.999	1.10179	
304		40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Divided	242.339	266.986	1.1017	

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/