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

    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/