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 Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 782 to 831 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    98 Squared trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 High confidence 1.55505 227160 146079
    Rooted deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] DNASE2B Low confidence 1.08981 173.58 189.17
    transcription factor lbx1. [swissprot;acc:p52954] LBX1 High confidence 1.29028 47.6504 36.9304
    99 Measured cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] no value Low confidence 1.10037 5752.65 6330.03
    s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] SKP1A High confidence 1.3705 2353.63 3225.65
    Ranked eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] EIF4B Low confidence 1.0798 200.497 185.679
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value High confidence 1.24949 88.2482 110.265
    Squared ras-related protein rab-37. [swissprot;acc:q96ax2] RAB37 Low confidence 1.17794 61163.4 51924
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] WDR33 High confidence 1.55382 226186 145568
    Rooted mosaic protein lgn. [swissprot;acc:p81274] GPSM2 1.29028 47.6504 36.9304
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] DVL3 Low confidence 1.08931 68.5805 74.7056
    100 Measured f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] FBXW7 High confidence 1.3705 2353.63 3225.65
    set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] SMYD2 Low confidence 1.10037 5752.65 6330.03
    Ranked b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] SLC7A9 1.0798 200.497 185.679
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 High confidence 1.24949 88.2482 110.265
    Squared cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] CPSF1 1.55382 226186 145568
    tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] TP53I3 Low confidence 1.17533 70019.5 82296.2
    Rooted natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] SLC11A1 1.08901 63.7749 69.4515
    regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] RGS17 High confidence 1.29028 47.6504 36.9304
    101 Measured cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2 1.3705 2353.63 3225.65
    set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] SMYD1 Low confidence 1.10037 5752.65 6330.03
    Ranked leucine zipper domain protein. [refseq;acc:nm_024589] ROGDI 1.07579 221.996 238.82
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 High confidence 1.24949 88.2482 110.265
    Squared cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] CPSF2 1.5507 222655 143584
    raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761] no value Low confidence 1.16811 63526.9 54384.3
    Rooted guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] GNAO1 High confidence 1.29028 47.6504 36.9304
    vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] VPS33A Low confidence 1.08881 69.1897 75.3346
    102 Measured presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] PSEN1 High confidence 1.3705 2353.63 3225.65
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 Low confidence 1.10006 5060.92 5567.34
    Ranked diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] DGKQ 1.07543 229.556 213.456
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 High confidence 1.24949 88.2482 110.265
    Squared cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] CD109 Low confidence 1.16767 54707.9 46852.3
    fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] FIP1L1 High confidence 1.54798 214143 138337
    Rooted diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] DGKQ Low confidence 1.08856 61.2565 66.6812
    rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] RAP1GAP High confidence 1.29028 47.6504 36.9304
    103 Measured 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] GOSR2 Low confidence 1.10006 5060.92 5567.34
    cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1 High confidence 1.3705 2353.63 3225.65
    Ranked trophinin. [swissprot;acc:q12816] TRO 1.24949 88.2482 110.265
    vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] PTPRA Low confidence 1.07538 203.948 189.652
    Squared 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] no value High confidence 1.54656 407289 263351
    zinc finger protein basonuclin. [swissprot;acc:q01954] BNC1 Low confidence 1.16733 105225 90141.3
    Rooted natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] SLC11A2 1.087 64.1217 69.7
    proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] FOS High confidence 1.27758 60.8365 77.7233
    104 Measured musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 1.36996 4241.57 5810.79
    ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Low confidence 1.10006 10618.8 11681.3
    Ranked adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 1.07377 219.277 204.212
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 High confidence 1.24926 252.371 202.016
    Squared cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] CPSF4 Low confidence 1.16546 60910.8 52263.5
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] PSCD1 High confidence 1.54656 407289 263351
    Rooted jun dimerization protein. [refseq;acc:nm_130469] no value 1.27758 60.8365 77.7233

    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/