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

    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/