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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1625 to 1674 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		green
    		network_comparison
    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
    1651 phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] PIK3R1
    1652 ring finger protein 38. [refseq;acc:nm_022781] RNF38
    1653 phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] PIK3R3
    1654 sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] SCAP
    1655 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] ATP5B
    1656 phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] PIK3R2
    1657 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] NUDT21 219.314 216.195 1.01443
    1658 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] ATP5A1 217.925 214.826
    1659 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] MRPS18A
    1660 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] EEA1 228.654 231.933 1.01434
    1661 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] ADSSL1 204.437 201.551 1.01432
    1662 transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] MORF4L2 228.477 231.747 1.01431
    1663 tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] TDO2 218.335 215.26 1.01429
    1664 transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] no value 228.484 231.74 1.01425
    1665 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] ADSS 204.433 201.564 1.01423
    1666 karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] TNPO2 218.679 215.612 1.01422
    1667 cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] CTSB 214.898 211.898 1.01416
    1668 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] no value 228.496 231.729 1.01415
    1669 ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]
    1670 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] RAC3
    1671 nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] NUP54
    1672 ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] RAC2
    1673 dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] MCM5
    1674 survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] SIP1

    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/