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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1675 to 1724 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    1675 probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] DDX20 228.496 231.729 1.01415
    1676 importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] TNPO1 218.691 215.645 1.01413
    1677 glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] GSTP1 218.654 221.732 1.01408
    1678 serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] SRPK3 216.899 213.889 1.01407
    1679 gtp binding protein 2. [refseq;acc:nm_019096] GTPBP2
    1680 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] CREBL1
    1681 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] FAM50B
    1682 sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] SRPK2
    1683 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] ATF6
    1684 sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] SRPK1
    1685 xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] FAM50A
    1686 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] OSGEPL1 220.75 217.704 1.01399
    1687 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] ATP5D 215.345 212.386 1.01393
    1688 transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] MORF4L1 228.523 231.703 1.01392
    1689 dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] DDX4 228.277 225.163 1.01383
    1690 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] RPS24 224.091 227.184 1.0138
    1691 translation initiation factor if-2. [swissprot;acc:o60841] EIF5B 217.263 214.315 1.01376
    1692 rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] RBM9 218.515 215.551 1.01375
    1693 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] IMPDH2 218.937 215.971 1.01373
    1694 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] GMPS
    1695 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] IMPDH1
    1696 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] PABPC3 217.624 214.69 1.01367
    1697 hskin17 protein. [refseq;acc:nm_012311] KIN
    1698 carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] CRAT
    1699 polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] PABPC4
    1700 polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] PABPC1
    1701 glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] G6PD 216.079 219.024 1.01363
    1702 dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] XRCC3
    1703 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] RECQL5
    1704 ataxin 2-binding protein. [swissprot;acc:q9nwb1] no value 218.514 215.577 1.01362
    1705 serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] PPP4C 223.846 220.847 1.01358
    1706 immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] IGBP1
    1707 mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] BUB1B 221.283 218.334 1.01351
    1708 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] PNPO
    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

    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/