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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Value Type Gene Rank green Interaction Map description Network Comparison Type Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 1730 to 1779 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
Rank
green
description
red
network_comparison
1730 212.567 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 215.336 1.01303
1731 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]
1732 aarf domain containing kinase 4. [refseq;acc:nm_024876]
1733 aarf domain containing kinase 1. [refseq;acc:nm_020421]
1734 219.081 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] 221.921 1.01296
1735 216.189 leucyl-trna synthetase. [refseq;acc:nm_020117] 218.99
1736 219.081 transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] 221.921
1737 216.189 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 218.99
1738 209.258 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] 206.595 1.01289
1739 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]
1740 defender against cell death 1 (dad-1). [swissprot;acc:p46966]
1741 t-complex 11. [refseq;acc:nm_018679]
1742 tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3]
1743 215.402 pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] 218.176 1.01288
1744 222.215 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] 219.423 1.01272
1745 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
1746 ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]
1747 190.845 tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] 188.452 1.0127
1748 212.971 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 215.673 1.01269
1749 203.485 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 206.058 1.01264
1750 213.57 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] 216.27
1751 223.97 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] 221.185 1.01259
1752 218.991 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 216.271 1.01258
1753 217.362 peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 220.091 1.01256
1754 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
1755 178.393 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 180.609 1.01242
1756 219.09 megf6 (fragment). [sptrembl;acc:o75095] 221.811
1757 178.325 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 180.537 1.0124
1758 230.595 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 233.45 1.01238
1759 222.086 ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] 219.37
1760 230.595 myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] 233.45
1761 myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590]
1762 nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380]
1763 myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649]
1764 myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]
1765 218.369 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 215.698
1766 231.732 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 228.932 1.01223
1767 198.86 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 201.288 1.01221
1768 187.534 estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] 185.276 1.01219
1769 225.734 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 223.016
1770 223.778 adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5] 221.082
1771 225.734 putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] 223.016
1772 225.739 spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] 223.032 1.01214
1773 spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082]
1774 phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394]
1775 210.274 serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] 207.757 1.01212
1776 214.286 nucleoporin like 1. [refseq;acc:nm_014089] 216.878 1.0121
1777 rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320]
1778 cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]
1779 203.874 pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 206.332 1.01206

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/