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 1330 to 1379 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    665 s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] SKP1A Low confidence 204.882 199.214 1.02845
    666 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] SOS2 200.639 195.092 1.02843
    transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] HES1 High confidence 229.072 216.576 1.0577
    667 ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] RNF144B Low confidence 208.62 202.855 1.02842
    delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] ECH1 High confidence 229.072 216.576 1.0577
    668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] ABLIM1
    inositol oxygenase (ec 1.13.99.1) (myo-inositol oxygenase) (aldehyde reductase-like 6) (renal-specific oxidoreductase) (kidney-specific protein 32). [swissprot;acc:q9ugb7] MIOX Low confidence 212.062 206.202 1.02842
    669 cytochrome p450 3a43 (ec 1.14.14.1). [swissprot;acc:q9hb55] CYP3A43 203.712 198.082
    synapsin i (brain protein 4.1). [swissprot;acc:p17600] SYN1 High confidence 229.072 216.576 1.0577
    670 autoantigen ngp-1. [swissprot;acc:q13823] GNL2 250.302 236.817 1.05694
    tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] no value Low confidence 204.551 198.901 1.02841
    671 integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] ITGB1 206.277 200.582 1.02839
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 High confidence 210.739 199.398 1.05688
    672 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] CYP3A7 Low confidence 203.727 198.116 1.02832
    nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 High confidence 210.739 199.398 1.05688
    673 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] DDX31 Low confidence 203.604 197.996 1.02832
    peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] CASK High confidence 226.497 214.355 1.05664
    674 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] PRSS7 Low confidence 204.81 199.174 1.0283
    hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] HIF3A High confidence 226.497 214.355 1.05664
    675 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] CYP3A5 Low confidence 203.702 198.095 1.0283
    single-minded homolog 1. [swissprot;acc:p81133] SIM1 High confidence 226.497 214.355 1.05664
    676 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] DUT Low confidence 202.698 197.124 1.02828
    dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] POLR2G High confidence 232.469 245.613 1.05654
    677 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] CCDC53 Low confidence 207.03 201.339 1.02827
    u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] LSM4 High confidence 228.944 216.745 1.05628
    678 cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] CYP3A4 Low confidence 203.747 198.152 1.02824
    sorting nexin 5. [swissprot;acc:q9y5x3] SNX5 High confidence 208.482 220.175 1.05609
    679 glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] YEATS4 Low confidence 198.424 192.974 1.02824
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value High confidence 132.413 125.389 1.05602
    680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4
    putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] EDEM2 Low confidence 196.228 190.844 1.02821
    681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 High confidence 132.413 125.389 1.05602
    sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] no value Low confidence 206.115 200.462 1.0282
    682 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] DDX54 204.263 198.663 1.02819
    homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value High confidence 132.413 125.389 1.05602
    683 doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 Low confidence 216.618 210.69 1.02814
    homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 High confidence 132.413 125.389 1.05602
    684 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5
    repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] no value Low confidence 199.669 194.204 1.02814
    685 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 High confidence 132.413 125.389 1.05602
    tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] TDO2 Low confidence 201.719 196.209 1.02808
    686 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value High confidence 132.413 125.389 1.05602
    neurogenin 2 (fragment). [swissprot;acc:q9h2a3] NEUROG2 Low confidence 216.554 210.642 1.02807
    687 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 High confidence 132.413 125.389 1.05602
    688 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] POLR2D 237.554 250.823 1.05586
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 Low confidence 216.552 210.641 1.02806
    689 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1
    t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 High confidence 135.379 128.225 1.05579
    690 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 Low confidence 216.552 210.641 1.02806

    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/