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 Gene Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 2875 to 2924 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		network_comparison
    		red
    		green
    360 Divided PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Squared 1.24054 9814.47 7911.48
    SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 1.09663 243.072 266.559
    Subtracted DDX24 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Rooted 6.723 46.901 53.624
    LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 985.34 4590.18 5575.52
    POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 19.906 240.287 260.193
    VAV2 vav-2 protein. [swissprot;acc:p52735] Squared 6292.8 31377.3 37670.1
    361 Divided CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Measured 1.17528 12787.6 10880.5
    MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Ranked 1.09644 242.83 266.248
    RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Rooted 1.10518 50.7801 45.9472
    SFPQ splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Squared 1.24047 70694.1 56989.9
    Subtracted CAPN2 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Rooted 6.6799 46.8525 53.5324
    CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Measured 983.3 6875.08 7858.38
    KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] Ranked 19.807 232.431 252.238
    TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Squared 6280 42363.8 36083.8
    362 Divided no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Rooted 1.10518 50.7803 45.9477
    CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Measured 1.17525 12786.6 10879.9
    SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Ranked 1.09641 231.492 211.136
    TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Squared 1.23973 57808.9 46630.3
    Subtracted no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 6265 34071.5 40336.5
    CAPN1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted 6.6791 46.8525 53.5316
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Measured 983.06 4981.52 5964.58
    KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Ranked 19.784 232.382 252.166
    363 Divided BOP1 block of proliferation 1. [swissprot;acc:q14137] Rooted 1.10477 49.4884 54.6735
    CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Measured 1.17509 12780.7 10876.4
    SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Ranked 1.09639 231.481 211.131
    TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Squared 1.23834 57579.2 46497.2
    Subtracted no value alpha-nac protein. [sptrembl;acc:q9h009] 6263.6 34069.4 40333
    CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Measured 981.59 6856.71 7838.3
    LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Rooted 6.639 56.48 63.119
    SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Ranked 19.658 233.539 253.197
    364 Divided DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Rooted 1.1047 50.0785 55.3215
    GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Measured 1.17334 5189 6088.47
    POLR2B dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Ranked 1.09625 243.208 266.617
    SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Squared 1.23817 17957.2 22234.1
    Subtracted no value dok-like protein. [refseq;acc:nm_024872] Measured 978.87 6102.59 7081.46
    CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Ranked 19.658 233.539 253.197
    DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Squared 6262.7 34068.1 40330.8
    GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Rooted 6.6304 60.594 67.2244
    365 Divided BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Squared 1.23807 17965.8 22243
    CAPS calcyphosine. [swissprot;acc:q13938] Measured 1.17334 5189 6088.47
    MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked 1.09609 242.744 266.07
    NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted 1.10428 49.7541 54.9425
    Subtracted DIRAS2 di-ras2. [refseq;acc:nm_017594] Squared 6262.7 34068 40330.7
    DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Measured 978.87 6102.59 7081.46
    FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked 19.658 233.539 253.197
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Rooted 6.6209 63.0715 56.4506
    366 Divided BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared 1.23628 62783.5 50784.1
    CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 1.17334 5189 6088.47
    RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Rooted 1.1042 50.5463 45.7763
    RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 1.09602 242.473 265.756

    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/