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 [...,...].
    Rank Value Type Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1625 to 1674 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		description
    		red
    		green
    		network_comparison
    407 Measured WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] 6603.41 7664.65 1.16071
    Ranked MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 1.08673
    Squared HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 18995.7 23244.9 1.22369
    Rooted no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 49.9856 45.4431 1.09996
    408 Measured dok-like protein. [refseq;acc:nm_024872] 6102.59 7081.46 1.1604
    Ranked CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 1.08649
    Squared HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 18995.7 23244.7 1.22368
    Rooted no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 49.9856 45.4432 1.09996
    409 Measured DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 6102.59 7081.46 1.1604
    Ranked POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] 241.045 261.874 1.08641
    Squared HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 18995.6 23242.8 1.22359
    Rooted MRPL3 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 50.4409 45.8795 1.09942
    410 Measured DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 6102.59 7081.46 1.1604
    Ranked no value 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 1.0864
    Squared BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 19546.1 23881.6 1.22181
    Rooted PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 55.5489 50.535 1.09922
    411 Measured FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 6102.59 7081.46 1.1604
    Ranked GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] 233.376 253.539 1.0864
    Squared SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 17861.2 21821.8 1.22174
    Rooted DUS1L pp3111 protein. [refseq;acc:nm_022156] 55.5489 50.535 1.09922
    412 Measured MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 3594.31 4169.95 1.16015
    Ranked UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] 240.788 261.416 1.08567
    Squared CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 19556 23891.8 1.22171
    Rooted STX18 syntaxin 18. [swissprot;acc:q9p2w9] 55.5489 50.535 1.09922
    413 Measured VAV1 vav proto-oncogene. [swissprot;acc:p15498] 6644.99 7707.8 1.15994
    Ranked POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] 240.913 261.45 1.08525
    Squared NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 19568.3 23904.6 1.2216
    Rooted no value rd protein. [swissprot;acc:p18615] 55.5489 50.535 1.09922
    414 Measured ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
    Ranked KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] 232.431 252.238 1.08522
    Squared DPM1 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] 22109.6 26989.4 1.22071
    Rooted GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 55.5489 50.535 1.09922
    415 Measured VAV3 vav-3 protein. [swissprot;acc:q9ukw4] 6647.43 7706.18 1.15927
    Ranked KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 232.382 252.166 1.08514
    Squared SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 29160.4 35570.2 1.21981
    Rooted AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 55.5489 50.535 1.09922
    416 Measured ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 4509.54 5223.95 1.15842
    Ranked POLR1B dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 240.6 261.041 1.08496
    Squared PHB prohibitin. [swissprot;acc:p35232] 22841.8 27856.2 1.21953
    Rooted ATP5F1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 55.5489 50.535 1.09922
    417 Measured BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 4522.71 5233.14 1.15708
    Ranked SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 233.539 253.197 1.08417
    Squared no value repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 22841.8 27856.2 1.21953
    Rooted DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] 55.5489 50.535 1.09922
    418 Measured BCAS2 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 5493.1 6350.19 1.15603
    Ranked CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 233.539 253.197 1.08417
    Squared ENOPH1 e-1 enzyme. [refseq;acc:nm_021204] 30903.8 37638.1 1.21791
    Rooted SNX13 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 55.5489 50.535 1.09922
    419 Measured CDC5L cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 5493.1 6350.19 1.15603
    Ranked FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 233.539 253.197 1.08417

    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/