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

    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/