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 Value Type Network Comparison Type description Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 925 to 974 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    116 MYH13 Squared myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] High confidence 19321 1.54043 12542.6
    PANK1 Measured pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 21185 1.34491 28492
    PSEN1 Rooted presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Low confidence 66.9562 1.08017 72.3243
    VPS18 Ranked vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] 204.161 1.07008 190.791
    117 CPSF3 Squared cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] High confidence 211446 1.53866 137422
    F13A1 Ranked coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Low confidence 226.395 1.06935 211.713
    HMG20A Rooted high-mobility group 20a. [refseq;acc:nm_018200] 69.2016 1.08014 74.7475
    JUNB transcription factor jun-b. [swissprot;acc:p17275] High confidence 63.4173 1.25409 79.5311
    MAGEA6 Measured melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Low confidence 11285.3 1.0937 10318.5
    NEURL Ranked neuralized-like. [refseq;acc:nm_004210] High confidence 332.326 1.24491 266.948
    PANK2 Measured pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 21185 1.34491 28492
    TMED10 Squared transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Low confidence 81950.4 1.14622 93933.1
    118 HOMER2 Rooted homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 50.3065 1.2519 62.9788
    NDN Measured necdin. [swissprot;acc:q99608] Low confidence 11285.3 1.0937 10318.5
    NDUFA12 Ranked nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] High confidence 284.753 1.24382 228.934
    PANK3 Measured pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 21185 1.34491 28492
    PAPOLA Squared poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 210445 1.53858 136779
    PIGB phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Low confidence 81950.4 1.14622 93933.1
    SENP8 Rooted sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 67.0736 1.08012 72.4478
    TGM1 Ranked protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] 226.395 1.06935 211.713
    119 COQ7 Rooted ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] High confidence 50.3247 1.25166 62.9892
    EXOC2 Squared exocyst complex component sec5. [swissprot;acc:q96kp1] 210335 1.53848 136716
    MAGED1 Measured melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Low confidence 11285.3 1.0937 10318.5
    NDUFS4 Ranked nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] High confidence 318.982 1.23157 259.004
    NEDD8 Rooted ubiquitin-like protein nedd8. [swissprot;acc:q15843] Low confidence 67.0736 1.08012 72.4478
    PCF11 Squared pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 58331.7 1.14295 51036
    SLC11A1 Ranked natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] 225.666 1.06897 211.107
    SLC25A43 Measured mitochondrial solute carrier protein. [refseq;acc:nm_145305] High confidence 21185 1.34491 28492
    120 CPSF3 Squared cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Low confidence 58384.8 1.14263 51096.7
    DVL1 Ranked segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 203.016 1.0687 189.965
    E2F1 Rooted 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] 64.712 1.07988 69.8815
    HMG20B Measured 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] High confidence 5136.78 1.34247 6895.98
    HOMER1 Rooted homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 50.3333 1.25154 62.9942
    KCND2 Ranked potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 269.278 1.21699 327.709
    MAGEF1 Measured melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Low confidence 11285.3 1.0937 10318.5
    PAPOLG Squared poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] High confidence 210199 1.53836 136638
    121 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Low confidence 43800.4 1.14188 38358.3
    CTH Ranked cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] High confidence 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 Rooted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 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 Measured transcription factor jun-b. [swissprot;acc:p17275] 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 Squared serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] High confidence 199594 1.53509 130021
    122 no value Measured melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Low confidence 11285.3 1.0937 10318.5
    Ranked nanos (fragment). [sptrembl;acc:q8wy41] 203.66 1.06785 217.479
    CSTF3 Squared cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] High confidence 201896 1.53061 131906
    CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Low confidence 82257.5 1.14052 72122.5
    HMG20A Measured high-mobility group 20a. [refseq;acc:nm_018200] High confidence 5140.14 1.34112 6893.53
    JUND Rooted transcription factor jun-d. [swissprot;acc:p17535] 63.636 1.25122 79.6225

    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/