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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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3458 to 3507 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1729 ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Divided 187.582 190.028 1.01304
1730 CABC1 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 215.336 212.567 1.01303
GATAD2A p66 alpha. [refseq;acc:nm_017660] Subtracted 167.687 170.455 2.768
1731 ADCK2 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Divided 215.336 212.567 1.01303
GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Subtracted 167.687 170.455 2.768
1732 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
ADCK4 aarf domain containing kinase 4. [refseq;acc:nm_024876] Divided 215.336 212.567 1.01303
1733 ADCK1 aarf domain containing kinase 1. [refseq;acc:nm_020421]
PFKL 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] Subtracted 240.32 243.085 2.765
1734 IMPA1 inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] 210.366 213.118 2.752
NOLA2 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Divided 221.921 219.081 1.01296
1735 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Subtracted 168.018 170.769 2.751
LARS leucyl-trna synthetase. [refseq;acc:nm_020117] Divided 218.99 216.189 1.01296
1736 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Subtracted 168.002 170.753 2.751
GTF2F1 transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Divided 221.921 219.081 1.01296
1737 LARS2 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 218.99 216.189
PFKM 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Subtracted 240.32 243.069 2.749
1738 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 168.098 170.844 2.746
LIPT1 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Divided 206.595 209.258 1.01289
1739 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Subtracted 168.091 170.837 2.746
TUBG1 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Divided 206.595 209.258 1.01289
1740 DAD1 defender against cell death 1 (dad-1). [swissprot;acc:p46966]
IMPA2 inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Subtracted 210.358 213.103 2.745
1741 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 168.145 170.888 2.743
TCP11 t-complex 11. [refseq;acc:nm_018679] Divided 206.595 209.258 1.01289
1742 MSRA peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Subtracted 220.091 217.362 2.729
TUBG2 tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] Divided 206.595 209.258 1.01289
1743 no value pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] 218.176 215.402 1.01288
PSAT1 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Subtracted 220.091 217.362 2.729
1744 MEGF6 megf6 (fragment). [sptrembl;acc:o75095] 221.811 219.09 2.721
SGPL1 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Divided 219.423 222.215 1.01272
1745 no value 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]
BARD1 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Subtracted 216.271 218.991 2.72
1746 MTAP 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 223.016 225.734 2.718
OAT ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Divided 219.423 222.215 1.01272
1747 ERCC2 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] 188.452 190.845 1.0127
FTSJ1 putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Subtracted 223.016 225.734 2.718
1748 no value bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Divided 215.673 212.971 1.01269
RUVBL1 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] Subtracted 219.37 222.086 2.716
1749 MLH3 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Divided 206.058 203.485 1.01264
SH3GL3 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Subtracted 206.823 204.111 2.712
1750 LIMCH1 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Divided 216.27 213.57 1.01264
SPTBN2 spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Subtracted 223.032 225.739 2.707
1751 AP1M2 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] Divided 221.185 223.97 1.01259
SPTBN1 spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Subtracted 223.032 225.739 2.707
1752 BARD1 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Divided 216.271 218.991 1.01258
PGM3 phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Subtracted 223.032 225.739 2.707
1753 ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 206.549 203.844 2.705
MSRA peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Divided 220.091 217.362 1.01256
1754 HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Subtracted 206.549 203.844 2.705

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
- 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/