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 [...,...].
    Hugo Rank Gene Value Type Network Comparison Type description Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1 to 50 of 8289 in total
    Hugo  : no value
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    2 mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] High confidence 15 28 1.86667
    13 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 37.9984 29.1831 1.30207
    23 implantation-associated protein. [refseq;acc:nm_032121] 198 163 1.21472
    28 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
    30 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] High confidence 187.457 243.678 1.29991
    41 protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 322 253 1.27273
    43 jun dimerization protein. [refseq;acc:nm_130469] 204.641 160.957 1.2714
    48 protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Low confidence 242.742 217.217 1.11751
    56 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] High confidence 266.856 336.233 1.25998
    58 jun dimerization protein. [refseq;acc:nm_130469] Low confidence 202.802 182.73 1.10985
    63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] High confidence 266.865 336.178 1.25973
    68 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 239.692 217.005 1.10455
    71 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 230.944 209.149 1.10421
    77 putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 195.851 215.424 1.09994
    84 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 226.338 207.874 1.08882
    85 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence 88.2482 110.265 1.24949
    88 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
    94 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
    99 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
    110 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Low confidence 197.752 212.031 1.07221
    122 nanos (fragment). [sptrembl;acc:q8wy41] 203.66 217.479 1.06785
    137 testican-3 precursor. [swissprot;acc:q9bq16] 220.395 234.389 1.0635
    138 transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] 218.36 205.4 1.0631
    147 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 50.7983 42.3003 1.2009
    149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718
    152 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 55 46 1.19565
    168 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 82.5916 98.0548 1.18722
    178 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 226.887 194.72 1.1652
    179 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 226.884 194.79 1.16476
    183 bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Low confidence 196.372 206.947 1.05385
    185 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 212.589 201.755 1.0537
    187 ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 189.373 179.829 1.05307
    191 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] High confidence 226.582 198.444 1.14179
    195 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Low confidence 211.679 222.623 1.0517
    206 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 211.457 222.138 1.05051
    215 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] High confidence 112 126 1.125
    221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
    238 rd protein. [swissprot;acc:p18615] 227.357 254.15 1.11785
    240 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 162.755 155.476 1.04682
    243 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
    247 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
    rna-binding protein. [refseq;acc:nm_019027] High confidence 237.302 212.41 1.11719
    248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
    263 sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581] Low confidence 216.546 207.063 1.0458
    271 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] High confidence 241.373 267.352 1.10763
    277 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 1.10665
    cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 211.912 202.965 1.04408
    281 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] High confidence 241.808 267.335 1.10557
    288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 266.078 1.10517
    289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 246.892 1.10486

    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/