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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1908 to 1957 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    120 CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared Divided Low confidence 58384.8 1.14263 51096.7
    DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked 203.016 1.0687 189.965
    E2F1 transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Rooted 64.712 1.07988 69.8815
    EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Measured Subtracted 6991.78 856.67 7848.45
    FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] High confidence 4932.27 2101.02 7033.29
    GNB3 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Rooted 40.081 14.9264 25.1546
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 69.2016 5.5459 74.7475
    HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Measured Divided High confidence 5136.78 1.34247 6895.98
    HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted 50.3333 1.25154 62.9942
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 269.278 1.21699 327.709
    MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured Low confidence 11285.3 1.0937 10318.5
    PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared High confidence 210199 1.53836 136638
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Ranked Subtracted 227.199 34.484 192.715
    121 no value intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Squared Low confidence 59879.6 7904.3 51975.3
    jun dimerization protein. [refseq;acc:nm_130469] Measured High confidence 4932.27 2101.02 7033.29
    ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Squared Divided Low confidence 43800.4 1.14188 38358.3
    ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Rooted Subtracted 61.0916 5.5442 66.6358
    CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared High confidence 81527.6 25337 56190.6
    CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked Divided 269.254 1.2169 327.655
    DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Low confidence 203.007 1.06854 189.985
    E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted 64.712 1.07988 69.8815
    HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 50.339 1.25147 62.9975
    JUNB transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 1.3422 7488.4
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Low confidence 11285.3 1.0937 10318.5
    PPP1CC serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared High confidence 199594 1.53509 130021
    PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Rooted Subtracted 63.6205 14.7367 48.8838
    SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Measured Low confidence 6991.78 856.67 7848.45
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked High confidence 227.202 34.379 192.823
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Low confidence 203.914 13.725 190.189
    122 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Measured Divided 11285.3 1.0937 10318.5
    nanos (fragment). [sptrembl;acc:q8wy41] Ranked 203.66 1.06785 217.479
    CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared Subtracted High confidence 81520.8 25332.3 56188.5
    CD109 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Low confidence 54707.9 7855.6 46852.3
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked High confidence 199.949 34.238 234.187
    CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared Divided 201896 1.53061 131906
    CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Low confidence 82257.5 1.14052 72122.5
    DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Rooted Subtracted 61.2565 5.4247 66.6812
    FOSL2 fos-related antigen 2. [swissprot;acc:p15408] Measured High confidence 4941.95 2095.16 7037.11
    HMG20A high-mobility group 20a. [refseq;acc:nm_018200] Divided 5140.14 1.34112 6893.53
    HMG20B high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Rooted Subtracted 60.9342 14.2045 75.1387
    JUND transcription factor jun-d. [swissprot;acc:p17535] Divided 63.636 1.25122 79.6225
    KCND3 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Ranked 269.248 1.21688 327.642
    PLK1 serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Rooted Low confidence 68.1979 1.07896 73.5829
    SLC16A3 monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Measured Subtracted 10325 853.2 11178.2
    VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Ranked 204.161 13.37 190.791
    123 ATG4A cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured Divided High confidence 24260.3 1.33503 18172.1
    BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared Low confidence 81989.8 1.14016 71910.8
    CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Subtracted High confidence 81478.9 25303.7 56175.2
    CTSZ cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] Rooted Divided Low confidence 68.1979 1.07896 73.5829
    DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Ranked 202.96 1.06768 190.094

    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/