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 [...,...].
    Gene Rank Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1330 to 1379 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Value Type
    		red
    		green
    		network_comparison
    167 AMPD2 Subtracted amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 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 Divided glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 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 Subtracted myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 2765.82 1723.37
    RAB24 Divided max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 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 Subtracted b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 69165.6 52992.1 16173.5
    CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked 312 284 28
    HSD17B14 Divided retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 173408 242989 1.40126
    PYGM Subtracted glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 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 Divided small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 56.3709 65.8949 1.16895
    169 no value Subtracted formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Measured 4245.52 5942.75 1697.23
    ATG3 Divided apg3p; pc3-96 protein. [refseq;acc:nm_022488] Ranked 82.5916 98.0548 1.18722
    CDK2AP1 Subtracted 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] 312 284 28
    COPS3 Divided cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 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 Subtracted pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 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 Divided symplekin. [swissprot;acc:q92797] Squared 124118 88668.8 1.39979
    170 no value Subtracted huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 4247.86 5941.88 1694.02
    B9D1 Divided b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Rooted 53.4993 45.9227 1.16499
    BCL6 Subtracted b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared 69165 52991.7 16173.3
    CTPS2 Divided cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 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 Subtracted protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted 55.6161 66.7332 11.1171
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked 227.971 200.417 27.554
    TIA1 Divided nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 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 Subtracted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 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 Divided nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked 227.202 192.823 1.17829
    TRPC4 Subtracted short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 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 Divided likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared 121579 87259.3 1.39331
    CTBP1 Subtracted c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 69123.3 52967 16156.3
    SF3B1 Divided splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Rooted 56.7592 65.9889 1.16261
    TBC1D10A Subtracted ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked 201.515 228.752 27.237
    TIPRL Divided cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 205.556 1.17685
    TRO trophinin. [swissprot;acc:q12816] Measured 23693.7 18263 1.29736
    173 no value Subtracted methyltransferase like 2. [refseq;acc:nm_018396] Squared 71576.8 56326.7 15250.1
    BCAR3 Divided breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Measured 4579.34 5940.64 1.29727
    MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Rooted 145.551 168.796 1.1597

    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/