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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1601 to 1650 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    1601 PMM2 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 217.268 213.842 1.01602
    1602 PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 217.334 213.914 1.01599
    1603 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 213.22 1.01595
    1604 CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 214.984 211.614 1.01593
    1605 FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 213.916 1.01592
    1606 APOA1BP apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 207.916 204.662 1.0159
    1607 CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] 214.982 211.622 1.01588
    1608 TMEM189 ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 208.106 204.867 1.01581
    1609 UGP2 utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 208.113 204.876 1.0158
    1610 UBE2V2 ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] 208.122 204.886 1.01579
    1611 CEP70 p10-binding protein. [refseq;acc:nm_024491] 221.313 217.877 1.01577
    1612 no value enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] 221.426 224.902 1.0157
    1613 HTATIP2 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] 182.378 185.241
    1614 FOXA2 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 217.233 213.897 1.0156
    1615 POLE2 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 246.38 242.596
    1616 NAGS n-acetylglutamate synthase. [refseq;acc:nm_153006] 223.179 226.611 1.01538
    1617 SHMT1 serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] 221.045 217.699 1.01537
    1618 TCEA2 transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] 227.768 231.246 1.01527
    1619 no value transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
    1620 GTF2B transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] 228.611 225.185 1.01521
    1621 ZNHIT3 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
    1622 NHP2L1 nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]
    1623 NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]
    1624 PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 230.643 227.194 1.01518
    1625 RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 217.446 214.2 1.01515
    1626 TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]
    1627 TMBIM1 pp1201 protein. [refseq;acc:nm_022152]
    1628 FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
    1629 no value sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]
    1630 SREBF1 sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]
    1631 GSPT1 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 218.789 215.533 1.01511
    1632 BUB3 mitotic checkpoint protein bub3. [swissprot;acc:o43684] 221.934 218.658 1.01498
    1633 ZNF207 zinc finger protein 207. [swissprot;acc:o43670]
    1634 MLYCD malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 215.772 212.596 1.01494
    1635 ITCH itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483]
    1636 BECN1 beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] 202.358 199.408 1.01479
    1637 PSMC5 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]
    1638 SHMT2 serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] 220.686 217.481 1.01474
    1639 VPS72 yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] 194.516 197.364 1.01464
    1640 HAGH hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
    1641 PSMB4 proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] 218.167 215.034 1.01457
    1642 CDC25B m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] 260.269 256.531
    1643 PNKD myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] 194.476 197.305 1.01455
    1644 no value secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 217.256 214.149 1.01451
    1645 PFDN1 prefoldin subunit 1. [swissprot;acc:o60925]
    1646 SMOC2 secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
    1647 CHDH choline dehydrogenase. [refseq;acc:nm_018397]
    1648 no value hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 219.745 222.928 1.01448
    1649 PRSS12 neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] 219.062 215.942 1.01445
    1650 RNF44 ring finger protein 44. [refseq;acc:nm_014901]

    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/