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 1325 to 1374 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    663 ITGA3 integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006] Low confidence 206.32 200.601 1.02851
    MRRF mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] High confidence 229.072 216.576 1.0577
    664 PEX5 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Low confidence 201.821 196.233 1.02848
    665 HEY2 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] High confidence 229.072 216.576 1.0577
    SKP1A 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] Low confidence 204.882 199.214 1.02845
    666 HES1 transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] High confidence 229.072 216.576 1.0577
    SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Low confidence 200.639 195.092 1.02843
    667 ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] High confidence 229.072 216.576 1.0577
    RNF144B ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] Low confidence 208.62 202.855 1.02842
    668 ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] High confidence 229.072 216.576 1.0577
    MIOX inositol oxygenase (ec 1.13.99.1) (myo-inositol oxygenase) (aldehyde reductase-like 6) (renal-specific oxidoreductase) (kidney-specific protein 32). [swissprot;acc:q9ugb7] Low confidence 212.062 206.202 1.02842
    669 CYP3A43 cytochrome p450 3a43 (ec 1.14.14.1). [swissprot;acc:q9hb55] 203.712 198.082
    SYN1 synapsin i (brain protein 4.1). [swissprot;acc:p17600] High confidence 229.072 216.576 1.0577
    670 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Low confidence 204.551 198.901 1.02841
    GNL2 autoantigen ngp-1. [swissprot;acc:q13823] High confidence 250.302 236.817 1.05694
    671 ITGB1 integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] Low confidence 206.277 200.582 1.02839
    NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] High confidence 210.739 199.398 1.05688
    672 CYP3A7 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Low confidence 203.727 198.116 1.02832
    NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] High confidence 210.739 199.398 1.05688
    673 CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 226.497 214.355 1.05664
    DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Low confidence 203.604 197.996 1.02832
    674 HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] High confidence 226.497 214.355 1.05664
    PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Low confidence 204.81 199.174 1.0283
    675 CYP3A5 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] 203.702 198.095
    SIM1 single-minded homolog 1. [swissprot;acc:p81133] High confidence 226.497 214.355 1.05664
    676 DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Low confidence 202.698 197.124 1.02828
    POLR2G dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] High confidence 232.469 245.613 1.05654
    677 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Low confidence 207.03 201.339 1.02827
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] High confidence 228.944 216.745 1.05628
    678 CYP3A4 cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Low confidence 203.747 198.152 1.02824
    SNX5 sorting nexin 5. [swissprot;acc:q9y5x3] High confidence 208.482 220.175 1.05609
    679 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 132.413 125.389 1.05602
    YEATS4 glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] Low confidence 198.424 192.974 1.02824
    680 EDEM2 putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] 196.228 190.844 1.02821
    HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] High confidence 132.413 125.389 1.05602
    681 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Low confidence 206.115 200.462 1.0282
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] High confidence 132.413 125.389 1.05602
    682 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
    DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Low confidence 204.263 198.663 1.02819
    683 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] 216.618 210.69 1.02814
    HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] High confidence 132.413 125.389 1.05602
    684 no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Low confidence 199.669 194.204 1.02814
    HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] High confidence 132.413 125.389 1.05602
    685 HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
    TDO2 tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Low confidence 201.719 196.209 1.02808
    686 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 132.413 125.389 1.05602
    NEUROG2 neurogenin 2 (fragment). [swissprot;acc:q9h2a3] Low confidence 216.554 210.642 1.02807
    687 HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] High confidence 132.413 125.389 1.05602
    NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Low confidence 216.554 210.642 1.02807

    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/