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 Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2708 to 2757 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		green
    		network_comparison
    677 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] LSM4 Ranked 228.944 216.745 1.05628
    678 myelin gene expression factor 2. [refseq;acc:nm_016132] MYEF2 Rooted 56.8369 52.8585 1.07527
    sorting nexin 5. [swissprot;acc:q9y5x3] SNX5 Ranked 208.482 220.175 1.05609
    surfeit locus protein 1. [swissprot;acc:q15526] SURF1 Squared 22335.8 26232.2 1.17445
    transcription factor btf3 homolog 3. [swissprot;acc:q13892] no value Measured 6938.22 7770.65 1.11998
    679 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] ADSSL1 6503.1 7282.94 1.11992
    dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] DPP6 Squared 22337.3 26234.1 1.17445
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value Ranked 132.413 125.389 1.05602
    putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Rooted 61.5558 66.1861 1.07522
    680 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] ADSS Measured 6503.03 7282.5 1.11986
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Ranked 132.413 125.389 1.05602
    seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] FAP Squared 22336.8 26233.5 1.17445
    t54 protein. [swissprot;acc:q92917] GPKOW Rooted 61.5558 66.1861 1.07522
    681 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] COX15 Squared 22335.8 26232.2 1.17445
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Ranked 132.413 125.389 1.05602
    oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] SLC15A2 Rooted 80.2562 86.277 1.07502
    ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 Measured 7170.83 8029.64 1.11976
    682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Ranked 132.413 125.389 1.05602
    protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] COX10 Squared 22335.8 26232.2 1.17445
    stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] CLEC11A Rooted 86.5959 93.0684 1.07474
    syntaxin 12. [refseq;acc:nm_177424] STX12 Measured 5552.92 6217.59 1.1197
    683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Ranked 132.413 125.389 1.05602
    sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] SH3GL1 Measured 7139.5 7994.06 1.11969
    tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] TAF7L Rooted 72.8809 78.3254 1.0747
    [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] PDK1 Squared 22328.1 26222.3 1.17441
    684 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] EIF3B Measured 4359.82 4880.99 1.11954
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Ranked 132.413 125.389 1.05602
    transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] TAF7 Rooted 72.9862 78.4342 1.07464
    [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] PDK2 Squared 22328.2 26222.4 1.17441
    685 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] HEMK1 Rooted 57.4644 61.7491 1.07456
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Ranked 132.413 125.389 1.05602
    metaxin 1. [swissprot;acc:q13505] MTX1 Measured 9327.58 10442.2 1.1195
    translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] TPT1 Squared 42363.8 36083.8 1.17404
    686 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 Measured 6920.69 7747.63 1.11949
    c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] CLEC3A Rooted 86.4264 92.8635 1.07448
    homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value Ranked 132.413 125.389 1.05602
    peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Squared 28982.3 34012.8 1.17357
    687 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] PRKAA2 Measured 6920.71 7747.65 1.11949
    meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] DMC1 Squared 24633.6 28893.6 1.17293
    putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] N6AMT1 Rooted 57.6308 61.9165 1.07436
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Ranked 132.413 125.389 1.05602
    688 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] PRKAA1 Measured 6920.67 7747.6 1.11949
    adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] AHCY Squared 22245.5 26087.5 1.17271
    dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] no value Rooted 60.7997 65.3199 1.07435
    dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] POLR2D Ranked 237.554 250.823 1.05586
    689 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] PRKAB2 Measured 6920.69 7747.63 1.11949
    dendritic cell protein. [refseq;acc:nm_006360] EIF3M Squared 33104 38818.5 1.17262
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Rooted 100.684 108.135 1.074
    t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 Ranked 135.379 128.225 1.05579
    690 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] PRKAG3 Measured 6920.69 7747.63 1.11949

    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/