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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1230 to 1279 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    308 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 Divided Low confidence 210.018 201.475 1.0424
    necdin. [swissprot;acc:q99608] NDN Subtracted High confidence 88.2482 110.265 22.0168
    rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] RAB3GAP2 Low confidence 212.262 203.991 8.271
    309 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] MAGED1 High confidence 88.2482 110.265 22.0168
    microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] no value Divided Low confidence 200.213 192.103 1.04222
    nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795] NDUFA9 Subtracted 205.75 197.484 8.266
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Divided High confidence 242.153 266.673 1.10126
    310 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] MAGEF1 Subtracted 88.2482 110.265 22.0168
    nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795] NDUFA9 Divided Low confidence 205.75 197.484 1.04186
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 High confidence 242.153 266.673 1.10126
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Subtracted Low confidence 202.122 193.867 8.255
    311 exocyst complex component exo70. [swissprot;acc:q9upt5] EXOC7 204.124 212.339 8.215
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B High confidence 88.2482 110.265 22.0168
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B Divided 242.627 267.151 1.10108
    ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] UBE1C Low confidence 192.088 184.374 1.04184
    312 60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L High confidence 242.195 266.663 1.10103
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value Subtracted 88.2482 110.265 22.0168
    transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] BACH1 Low confidence 172.647 164.44 8.207
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] SNRPA1 Divided 202.051 193.937 1.04184
    313 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] no value 202.05 193.94 1.04182
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 Subtracted High confidence 88.2482 110.265 22.0168
    nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] NFE2L2 Low confidence 172.647 164.44 8.207
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B Divided High confidence 232.473 211.207 1.10069
    314 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Subtracted 88.2482 110.265 22.0168
    methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] METAP1 Divided 244.126 268.604 1.10027
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Low confidence 202.057 193.952 1.04179
    transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] BACH2 Subtracted 172.647 164.44 8.207
    315 glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5] SNORD23 207.402 199.219 8.183
    melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 High confidence 88.2482 110.265 22.0168
    methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] METAP2 Divided 244.126 268.604 1.10027
    tankyrase 1 (ec 2.4.2.30) (tank1) (tankyrase i) (tnks-1) (trf1- interacting ankyrin-related adp-ribose polymerase). [swissprot;acc:o95271] TNKS Low confidence 214.067 205.509 1.04164
    316 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Subtracted High confidence 88.2482 110.265 22.0168
    potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] KCNA2 Divided Low confidence 209.583 201.251 1.0414
    protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] EIF1 High confidence 242.694 267.017 1.10022
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] SNRPA1 Subtracted Low confidence 202.051 193.937 8.114
    317 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] no value High confidence 88.2482 110.265 22.0168
    microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Low confidence 200.213 192.103 8.11
    potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] KCNA1 Divided 209.58 201.251 1.04139
    splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] no value High confidence 224.445 204.044 1.09998
    318 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Subtracted Low confidence 202.05 193.94 8.11
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 High confidence 88.2482 110.265 22.0168
    mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] MRPL3 Divided 242.011 266.18 1.09987
    potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] KCNA4 Low confidence 209.579 201.251 1.04138
    319 60s ribosomal protein l19. [swissprot;acc:p14118] RPL19 High confidence 240.73 264.729 1.09969
    heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082] HSPB2 Low confidence 212.752 204.328 1.04123
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Subtracted High confidence 88.2482 110.265 22.0168
    mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] MRPL44 Low confidence 216.283 208.173 8.11
    320 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] CDH1 Divided High confidence 241.892 265.96 1.0995
    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 Subtracted 88.2482 110.265 22.0168
    phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735] PHKG2 Divided Low confidence 217.756 226.722 1.04117

    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/