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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2563 to 2612 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		red
    		green
    		network_comparison
    641 PRAM1 Ranked pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 217.67 230.596 1.05938
    SYN1 Rooted synapsin i (brain protein 4.1). [swissprot;acc:p17600] 60.0129 64.7371 1.07872
    642 no value Ranked intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 217.67 230.596 1.05938
    ATPIF1 Measured atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] 4810.85 5414.23 1.12542
    PFKL Squared 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 16123.9 19009.7 1.17898
    SORBS1 Rooted ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 64.4857 69.5606 1.0787
    643 ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 87.4586 81.0798 1.07867
    HRBL Ranked hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] 217.67 230.596 1.05938
    PFKM Squared 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 16126.5 19012.6 1.17897
    SMOX Measured polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] 4810.85 5414.23 1.12542
    644 C16orf35 Ranked cgthba protein (-14 gene protein). [swissprot;acc:q12980] 217.67 230.596 1.05938
    HCCS Measured cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 4810.85 5414.22 1.12542
    PFKP Squared 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 16156.3 19046 1.17886
    POLR1E Rooted rna polymerase i associated factor 53. [refseq;acc:nm_022490] 51.1896 47.4617 1.07855
    645 no value Squared nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 22722.5 26786.5 1.17885
    GSTT1 Measured glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 4810.71 5413.89 1.12538
    HTATSF1 Ranked hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] 217.67 230.596 1.05938
    MOBKL3 Rooted preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 63.1463 68.1044 1.07852
    646 no value Squared 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 27898 32866.2 1.17808
    DNAJB11 Rooted dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] 63.1463 68.1044 1.07852
    FBL Measured fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 4019.88 4522.61 1.12506
    SCOC Ranked short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] 216.731 229.549 1.05914
    647 CAPNS1 Rooted calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 64.5657 69.6237 1.07834
    CTSB Squared cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 33384.2 39324.9 1.17795
    DYNLL2 Ranked dynein light chain 2. [refseq;acc:nm_080677] 216.731 229.549 1.05914
    TRPC4 Measured short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 5167.88 4594.43 1.12481
    648 ARID1A Rooted swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 64.5685 69.6269 1.07834
    MARS Ranked methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 218.227 206.078 1.05895
    RBL1 Squared retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 29174 34363.5 1.17788
    SF3A3 Measured splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] 5248.07 5901.72 1.12455
    649 EIF4E Ranked eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 233.725 220.751 1.05877
    GCA Rooted grancalcin. [swissprot;acc:p28676] 64.5659 69.624 1.07834
    RBL2 Squared retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 29173.8 34362.7 1.17786
    SF3A1 Measured splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] 5248.07 5901.72 1.12455
    650 no value Ranked u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 228.986 216.276 1.05877
    CDYL2 Squared chromodomain y-like protein 2. [refseq;acc:nm_152342] 29016.1 34169.2 1.17759
    GORASP2 Measured golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 8362.81 9402.7 1.12435
    SRI Rooted sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 64.566 69.6241 1.07834
    651 BAIAP3 Ranked bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 233.725 220.751 1.05877
    CDY1B Squared testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 29012.2 34163.9 1.17757
    PDCD6 Rooted programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 64.5685 69.6269 1.07834
    TBC1D10A Measured ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 5168.43 4597.44 1.1242
    652 no value Ranked tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 248.994 235.255 1.0584
    ARID1B Rooted brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 64.5672 69.6254 1.07834
    CDYL Squared chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] 29012.2 34163.9 1.17757
    TRPC5 Measured short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 5168.43 4597.44 1.1242
    653 no value Ranked dok-like protein. [refseq;acc:nm_024872] 216.504 204.622 1.05807
    CDY2B Squared testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 29012.4 34164 1.17757
    MARS Measured methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 5560.06 6248.27 1.12378
    SORBS2 Rooted arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 64.4927 69.539 1.07825

    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/