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 2501 to 2550 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    626 GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Divided High confidence 214.256 202.14 1.05994
    HEYL hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Subtracted 229.072 216.576 12.496
    HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Divided Low confidence 204.239 198.436 1.02924
    Subtracted 5.803
    627 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 204.234 198.433 5.801
    JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Divided High confidence 214.256 202.139 1.05994
    P4HB protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Low confidence 204.369 198.564 1.02923
    SYN2 synapsin ii. [swissprot;acc:q92777] Subtracted High confidence 229.072 216.576 12.496
    628 no value histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Divided Low confidence 204.234 198.433 1.02923
    CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Subtracted 203.853 198.057 5.796
    GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Divided High confidence 214.256 202.14 1.05994
    MRRF mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Subtracted 229.072 216.576 12.496
    629 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Low confidence 204.242 198.448 5.794
    GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Divided High confidence 214.256 202.14 1.05994
    P4HA1 prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Low confidence 204.369 198.564 1.02923
    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] Subtracted High confidence 229.072 216.576 12.496
    630 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Low confidence 204.242 198.448 5.794
    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 12.496
    NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Divided 214.256 202.141 1.05993
    P4HA2 prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Low confidence 204.369 198.564 1.02923
    631 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 204.242 198.448 1.0292
    HES1 transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Subtracted High confidence 229.072 216.576 12.496
    MARCH6 similar to s. cerevisiae ssm4. [refseq;acc:nm_005885] Low confidence 207.662 201.876 5.786
    PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Divided High confidence 214.256 202.141 1.05993
    632 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Low confidence 204.242 198.448 1.0292
    large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Subtracted 207.662 201.876 5.786
    ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] High confidence 229.072 216.576 12.496
    HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Divided 214.254 202.166 1.05979
    633 no value dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [swissprot;acc:q92685] Subtracted Low confidence 200.085 194.301 5.784
    AARS alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Divided High confidence 234.106 248.104 1.05979
    ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Subtracted 229.072 216.576 12.496
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Divided Low confidence 203.734 197.956 1.02919
    634 no value dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] High confidence 226.523 213.786 1.05958
    SYN1 synapsin i (brain protein 4.1). [swissprot;acc:p17600] Subtracted 229.072 216.576 12.496
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Low confidence 203.734 197.956 5.778
    TSC22D4 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Divided 203.726 197.955 1.02915
    635 BBS7 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 207.763 201.882 1.02913
    MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Subtracted High confidence 235.296 247.673 12.377
    RPL37 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Divided 228.639 242.258 1.05957
    TSC22D4 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Subtracted Low confidence 203.726 197.955 5.771
    636 N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 204.933 199.164 5.769
    RBM19 probable rna-binding protein kiaa0682. [swissprot;acc:q9y4c8] Divided 206.001 200.193 1.02901
    SFRS1 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] High confidence 228.639 242.258 1.05957
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Subtracted 212.2 199.849 12.351
    637 AGPAT3 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Divided Low confidence 192.166 186.751 1.029
    PPAT amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] High confidence 228.639 242.258 1.05957
    RNF144B ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] Subtracted Low confidence 208.62 202.855 5.765
    VAV3 vav-3 protein. [swissprot;acc:q9ukw4] High confidence 212.253 199.908 12.345
    638 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] Divided Low confidence 203.825 198.081 1.029
    SNX17 sorting nexin 17. [swissprot;acc:q15036] High confidence 228.639 242.258 1.05957

    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/