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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1708 to 1757 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		network_comparison
    		green
    1708 PNPO pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 221.283 1.01351 218.334
    1709 HHEX homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] 198.014 1.01346 195.385
    1710 no value casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 227.225 1.01345 224.21
    1711 HLCS biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 218.436 1.01337 215.553
    1712 TAF11 transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] 208.598 1.01331 211.375
    1713 SH3GL3 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 206.823 1.01329 204.111
    1714 ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 206.549 1.01327 203.844
    1715 HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]
    1716 SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 206.522 203.818
    1717 OSGEP o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] 221.058 218.164
    1718 SH3GL1 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 206.251 1.01325 203.553
    1719 no value helicase (fragment). [sptrembl;acc:q92771] 187.204 1.01322 189.679
    1720 DDX12 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 187.205
    1721 CSNK1D casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 227.125 1.01321 224.164
    1722 RPS13 40s ribosomal protein s13. [swissprot;acc:q02546] 220.899 1.01319 223.813
    1723 NADK putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 212.36 1.01312 215.147
    1724 IPMK inositol polyphosphate multikinase. [refseq;acc:nm_152230] 217.676 1.01311 220.53
    1725 AFG3L2 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]
    1726 FUT8 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5]
    1727 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 1.01308 213.118
    1728 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] 210.358 1.01305 213.103
    1729 ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 187.582 1.01304 190.028
    1730 CABC1 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] 215.336 1.01303 212.567
    1731 ADCK2 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]
    1732 ADCK4 aarf domain containing kinase 4. [refseq;acc:nm_024876]
    1733 ADCK1 aarf domain containing kinase 1. [refseq;acc:nm_020421]
    1734 NOLA2 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] 221.921 1.01296 219.081
    1735 LARS leucyl-trna synthetase. [refseq;acc:nm_020117] 218.99 216.189
    1736 GTF2F1 transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] 221.921 219.081
    1737 LARS2 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 218.99 216.189
    1738 LIPT1 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] 206.595 1.01289 209.258
    1739 TUBG1 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]
    1740 DAD1 defender against cell death 1 (dad-1). [swissprot;acc:p46966]
    1741 TCP11 t-complex 11. [refseq;acc:nm_018679]
    1742 TUBG2 tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3]
    1743 no value pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] 218.176 1.01288 215.402
    1744 SGPL1 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] 219.423 1.01272 222.215
    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]
    1746 OAT ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181]
    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 1.0127 190.845
    1748 no value 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 212.971
    1749 MLH3 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 206.058 1.01264 203.485
    1750 LIMCH1 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] 216.27 213.57
    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] 221.185 1.01259 223.97
    1752 BARD1 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 216.271 1.01258 218.991
    1753 MSRA 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 217.362
    1754 PSAT1 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
    1755 CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 180.609 1.01242 178.393
    1756 MEGF6 megf6 (fragment). [sptrembl;acc:o75095] 221.811 219.09
    1757 CTPS2 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 178.325

    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/