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 description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1708 to 1757 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1708 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] PNPO 221.283 218.334 1.01351
    1709 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] HHEX 198.014 195.385 1.01346
    1710 casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] no value 227.225 224.21 1.01345
    1711 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] HLCS 218.436 215.553 1.01337
    1712 transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] TAF11 208.598 211.375 1.01331
    1713 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] SH3GL3 206.823 204.111 1.01329
    1714 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] ARMET 206.549 203.844 1.01327
    1715 histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] HDC
    1716 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] SH3GL2 206.522 203.818
    1717 o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] OSGEP 221.058 218.164
    1718 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] SH3GL1 206.251 203.553 1.01325
    1719 helicase (fragment). [sptrembl;acc:q92771] no value 187.204 189.679 1.01322
    1720 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] DDX12 187.205
    1721 casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] CSNK1D 227.125 224.164 1.01321
    1722 40s ribosomal protein s13. [swissprot;acc:q02546] RPS13 220.899 223.813 1.01319
    1723 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] NADK 212.36 215.147 1.01312
    1724 inositol polyphosphate multikinase. [refseq;acc:nm_152230] IPMK 217.676 220.53 1.01311
    1725 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] AFG3L2
    1726 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] FUT8
    1727 inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] IMPA1 210.366 213.118 1.01308
    1728 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] IMPA2 210.358 213.103 1.01305
    1729 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] ATG12 187.582 190.028 1.01304
    1730 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] CABC1 215.336 212.567 1.01303
    1731 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] ADCK2
    1732 aarf domain containing kinase 4. [refseq;acc:nm_024876] ADCK4
    1733 aarf domain containing kinase 1. [refseq;acc:nm_020421] ADCK1
    1734 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] NOLA2 221.921 219.081 1.01296
    1735 leucyl-trna synthetase. [refseq;acc:nm_020117] LARS 218.99 216.189
    1736 transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] GTF2F1 221.921 219.081
    1737 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] LARS2 218.99 216.189
    1738 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] LIPT1 206.595 209.258 1.01289
    1739 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] TUBG1
    1740 defender against cell death 1 (dad-1). [swissprot;acc:p46966] DAD1
    1741 t-complex 11. [refseq;acc:nm_018679] TCP11
    1742 tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] TUBG2
    1743 pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] no value 218.176 215.402 1.01288
    1744 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] SGPL1 219.423 222.215 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] no value
    1746 ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] OAT
    1747 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] ERCC2 188.452 190.845 1.0127
    1748 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] no value 215.673 212.971 1.01269
    1749 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] MLH3 206.058 203.485 1.01264
    1750 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] LIMCH1 216.27 213.57
    1751 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] AP1M2 221.185 223.97 1.01259
    1752 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] BARD1 216.271 218.991 1.01258
    1753 peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] MSRA 220.091 217.362 1.01256
    1754 phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] PSAT1
    1755 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS 180.609 178.393 1.01242
    1756 megf6 (fragment). [sptrembl;acc:o75095] MEGF6 221.811 219.09
    1757 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 180.537 178.325 1.0124

    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/