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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1325 to 1374 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    166 NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Divided Ranked 209.299 249.187 1.19058
    NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Subtracted 312 284 28
    PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 4489.19 2765.82 1723.37
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 54.9787 66.2416 11.2629
    167 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Divided Squared 173408 242989 1.40126
    AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Subtracted Ranked 133 105 28
    CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Squared 64975.9 81151.2 16175.3
    FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Rooted 55.6161 66.7332 11.1171
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Divided Ranked 209.299 249.187 1.19058
    MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Measured 23693.7 18263 1.29736
    MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Subtracted 4489.19 2765.82 1723.37
    RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided Rooted 55.65 65.1448 1.17062
    168 no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked 82.5916 98.0548 1.18722
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured 23693.7 18263 1.29736
    BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Subtracted Squared 69165.6 52992.1 16173.5
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked 312 284 28
    HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Divided Squared 173408 242989 1.40126
    PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Subtracted Measured 4489.19 2765.82 1723.37
    REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Rooted 55.6161 66.7332 11.1171
    SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Divided 56.3709 65.8949 1.16895
    169 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted Measured 4245.52 5942.75 1697.23
    ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided Ranked 82.5916 98.0548 1.18722
    CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Subtracted 312 284 28
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Divided Rooted 62.762 53.7761 1.1671
    MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Measured 23693.7 18263 1.29736
    PASK pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Subtracted Squared 69165 52991.7 16173.3
    PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted 55.6161 66.7332 11.1171
    SYMPK symplekin. [swissprot;acc:q92797] Divided Squared 124118 88668.8 1.39979
    170 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted Measured 4247.86 5941.88 1694.02
    B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Divided Rooted 53.4993 45.9227 1.16499
    BCL6 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Subtracted Squared 69165 52991.7 16173.3
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Divided 96730.5 69286.7 1.39609
    MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Measured 23693.7 18263 1.29736
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Subtracted Rooted 55.6161 66.7332 11.1171
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked 227.971 200.417 27.554
    TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 227.199 192.715 1.17894
    171 CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared 96602.7 69211.2 1.39577
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted 61.6639 71.7355 1.16333
    MAGED2 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] Measured 23693.7 18263 1.29736
    NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted 4117.67 5801.04 1683.37
    SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared 69165 52991.7 16173.3
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 66.7332 11.1171
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided Ranked 227.202 192.823 1.17829
    TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Subtracted 201.478 228.784 27.306
    172 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Rooted 55.6161 66.7332 11.1171
    serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Measured 4556.78 2945.26 1611.52
    CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Divided Squared 121579 87259.3 1.39331
    CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Subtracted 69123.3 52967 16156.3
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided Rooted 56.7592 65.9889 1.16261
    TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Subtracted Ranked 201.515 228.752 27.237

    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/