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 description Hugo Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1341 to 1390 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		green
    		network_comparison
    168 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value Divided Measured 23693.7 18263 1.29736
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Squared 173408 242989 1.40126
    rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Subtracted Rooted 55.6161 66.7332 11.1171
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Divided 56.3709 65.8949 1.16895
    169 apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 Ranked 82.5916 98.0548 1.18722
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 Rooted 62.762 53.7761 1.1671
    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] CDK2AP1 Subtracted Ranked 312 284 28
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] no value Measured 4245.52 5942.75 1697.23
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Divided 23693.7 18263 1.29736
    pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] PASK Subtracted Squared 69165 52991.7 16173.3
    protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Rooted 55.6161 66.7332 11.1171
    symplekin. [swissprot;acc:q92797] SYMPK Divided Squared 124118 88668.8 1.39979
    170 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] BCL6 Subtracted 69165 52991.7 16173.3
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 Divided Rooted 53.4993 45.9227 1.16499
    cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 Squared 96730.5 69286.7 1.39609
    huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B Subtracted Ranked 227.971 200.417 27.554
    huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] no value Measured 4247.86 5941.88 1694.02
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Divided 23693.7 18263 1.29736
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 Ranked 227.199 192.715 1.17894
    protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Subtracted Rooted 55.6161 66.7332 11.1171
    171 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS Divided Squared 96602.7 69211.2 1.39577
    dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] NCBP2L Subtracted Measured 4117.67 5801.04 1683.37
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 Divided Rooted 61.6639 71.7355 1.16333
    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 Measured 23693.7 18263 1.29736
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 Ranked 227.202 192.823 1.17829
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] TRPC4 Subtracted 201.478 228.784 27.306
    u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Rooted 55.6161 66.7332 11.1171
    zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] SNAI2 Squared 69165 52991.7 16173.3
    172 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] CTBP1 69123.3 52967 16156.3
    cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL Divided Ranked 174.667 205.556 1.17685
    ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] TBC1D10A Subtracted 201.515 228.752 27.237
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] no value Rooted 55.6161 66.7332 11.1171
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T Divided Squared 121579 87259.3 1.39331
    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] no value Subtracted Measured 4556.78 2945.26 1611.52
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Divided Rooted 56.7592 65.9889 1.16261
    trophinin. [swissprot;acc:q12816] TRO Measured 23693.7 18263 1.29736
    173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Rooted 145.551 168.796 1.1597
    breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] BCAR3 Measured 4579.34 5940.64 1.29727
    methyltransferase like 2. [refseq;acc:nm_018396] no value Subtracted Squared 71576.8 56326.7 15250.1
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 Rooted 37.3005 48.4141 11.1136
    septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] SEPT4 Divided Squared 82624.3 115061 1.39258
    short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] TRPC5 Subtracted Ranked 201.515 228.752 27.237
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Divided 227.032 193.056 1.17599
    uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] PPP2R2D Subtracted Measured 4556.79 2945.28 1611.51
    174 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] DYNLT1 Squared 71576.8 56326.7 15250.1
    dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] DGCR14 Divided Ranked 335 286 1.17133
    luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] LUC7L2 Subtracted 228.1 200.968 27.132
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Divided Measured 4455.95 5774.03 1.2958
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] PANK1 Rooted 145.551 168.796 1.1597
    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 Subtracted 37.3005 48.4141 11.1136

    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/