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 [...,...].
    Network Comparison Type Hugo Rank Gene Value Type green red Filtered network_comparison description Interaction Map
    Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
    Network Comparison Type  : Divided
    Hugo  : no value
    Value Type  : Ranked
    Filtered  : 1
    Interaction Map  : High confidence
    Rank
    		green
    		red
    		network_comparison
    		description
    2 28 15 1.86667 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]
    30 243.678 187.457 1.29991 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]
    41 253 322 1.27273 protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]
    43 160.957 204.641 1.2714 jun dimerization protein. [refseq;acc:nm_130469]
    56 336.233 266.856 1.25998 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]
    63 336.178 266.865 1.25973 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]
    85 110.265 88.2482 1.24949 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
    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]
    147 42.3003 50.7983 1.2009 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]
    149 170 142 1.19718 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]
    152 46 55 1.19565 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
    168 98.0548 82.5916 1.18722 gaba-a receptor-associated protein. [sptrembl;acc:q9by60]
    178 194.72 226.887 1.1652 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]
    179 194.79 226.884 1.16476 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]
    191 198.444 226.582 1.14179 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
    215 126 112 1.125 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]
    221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
    238 254.15 227.357 1.11785 rd protein. [swissprot;acc:p18615]
    247 212.41 237.302 1.11719 rna-binding protein. [refseq;acc:nm_019027]
    248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
    271 267.352 241.373 1.10763 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]
    277 267.642 241.849 1.10665 40s ribosomal protein s29. [swissprot;acc:p30054]
    281 267.335 241.808 1.10557 60s ribosomal protein l17 (l23). [swissprot;acc:p18621]
    288 266.078 240.758 1.10517 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]
    289 246.892 272.781 1.10486 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]
    293 265.717 240.782 1.10356 60s ribosomal protein l23 (l17). [swissprot;acc:p23131]
    297 259.984 235.727 1.1029 60s ribosomal protein l7. [swissprot;acc:p18124]
    304 266.986 242.339 1.1017 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]
    306 266.673 242.153 1.10126 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]
    317 204.044 224.445 1.09998 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]
    321 265.959 241.892 1.09949 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]
    323 265.945 241.884 1.09947 60s ribosomal protein l23a. [swissprot;acc:p29316]
    337 267.527 243.583 1.0983 60s ribosomal protein l12. [swissprot;acc:p30050]
    338 267.528 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]
    339 267.527 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]
    341 263.798 240.243 1.09805 60s ribosomal protein l9. [swissprot;acc:p32969]
    344 265.136 241.625 1.0973 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
    348 265.696 242.14 1.09728 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]
    356 266.796 243.24 1.09684 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]
    357 266.661 243.12 1.09683 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]
    372 170.42 186.52 1.09447 ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
    380 264.79 242.109 1.09368 suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]
    387 264.11 242.238 1.09029 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
    388 208.756 227.575 1.09015 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]
    396 262.34 240.801 1.08945 putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]
    406 244.304 265.634 1.08731 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]
    410 253.539 233.376 1.0864 tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]
    452 207.972 224.161 1.07784 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]

    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/