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

    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/