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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2051 to 2100 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    Value Type
    description
    red
    green
    network_comparison
    513 Squared transforming protein rhoc (h9). [swissprot;acc:p08134] 19987.6 23960.7 1.19878
    Rooted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 51.5881 47.3127 1.09036
    514 Measured 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 7477 8532.02 1.1411
    Ranked segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 218.613 204.382 1.06963
    Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 19987.6 23960.7 1.19878
    Rooted xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 58.7805 64.0772 1.09011
    515 Measured transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 3890.53 4439.07 1.14099
    Ranked pescadillo homolog 1. [swissprot;acc:o00541] 251.297 234.941 1.06962
    Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 19987.6 23960.7 1.19878
    Rooted u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 56.3551 61.4322 1.09009
    516 Measured n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 4910.6 5600.61 1.14051
    Ranked u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 228.255 213.422 1.0695
    Squared transforming protein rhoa (h12). [swissprot;acc:p06749] 19987.6 23960.7 1.19878
    Rooted adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 50.7935 46.6042 1.08989
    517 Measured galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 4910.6 5600.61 1.14051
    Ranked metaxin 2. [swissprot;acc:o75431] 219.537 234.793 1.06949
    Squared splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 19263.3 23092.3 1.19877
    Rooted eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 50.0578 54.5502 1.08974
    518 Measured udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] 4910.6 5600.61 1.14051
    Ranked nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 250.858 234.563 1.06947
    Squared proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 11447.3 13719.2 1.19847
    Rooted trinucleotide repeat containing 15. [refseq;acc:nm_015575] 50.0578 54.5502 1.08974
    519 Measured glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 9648.27 10994.9 1.13957
    Ranked segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 218.702 204.582 1.06902
    Squared polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 22387.1 26827.3 1.19834
    Rooted septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 114.309 124.527 1.08939
    520 Measured endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 9642.22 10986.4 1.13941
    Ranked sqv-7-like protein (fragment). [sptrembl;acc:o95454] 214.754 229.565 1.06897
    Squared paxillin. [swissprot;acc:p49023] 22387.1 26827.3 1.19834
    Rooted breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 61.1902 66.6503 1.08923
    521 Measured u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 5390.78 6142.07 1.13937
    Ranked exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 215.237 230.07 1.06891
    Squared carboxypeptidase a5. [refseq;acc:nm_080385] 53174 44377.4 1.19822
    Rooted cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 61.1902 66.6503 1.08923
    522 Measured glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 9634.98 10976.2 1.1392
    Ranked pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 222.893 208.523 1.06891
    Squared carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 53174 44377.4 1.19822
    Rooted septin 10 isoform 1. [refseq;acc:nm_144710] 113.733 123.871 1.08914
    523 Measured aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 10640.2 12117.8 1.13887
    Ranked exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] 215.237 230.07 1.06891
    Squared neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] 53174 44377.4 1.19822
    Rooted ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 66.377 72.2842 1.08899
    524 Measured aquaporin 5. [swissprot;acc:p55064] 10640 12117.6 1.13887
    Ranked exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] 215.237 230.07 1.06891
    Squared aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] 53174 44377.4 1.19822
    Rooted brain protein 44. [swissprot;acc:o95563] 113.374 123.463 1.08899
    525 Measured lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 10639.8 12117.3 1.13887
    Ranked exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] 215.237 230.07 1.06891
    Squared carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 53174 44377.4 1.19822
    Rooted septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 113.374 123.463 1.08899

    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
    - 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/