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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1201 to 1250 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    301 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] ALG1 Divided High confidence 150.982 1.10193 166.372
    kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] KCNIP2 Subtracted Low confidence 213.976 8.336 222.312
    large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] SLC7A8 Divided 205.154 1.04287 196.72
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 Subtracted High confidence 88.2482 22.0168 110.265
    302 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 Divided 242.326 1.10185 267.008
    hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 Subtracted 88.2482 22.0168 110.265
    potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] KCNA2 Low confidence 209.583 8.332 201.251
    xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] XPR1 Divided 209.12 1.04274 200.548
    303 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 High confidence 242.333 1.10179 266.999
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] HOMER3 Low confidence 210.057 1.04273 201.45
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value Subtracted High confidence 88.2482 22.0168 110.265
    potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] KCNA1 Low confidence 209.58 8.329 201.251
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value Divided High confidence 242.339 1.1017 266.986
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] KHDRBS1 Low confidence 209.232 1.04271 200.662
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 Subtracted High confidence 88.2482 22.0168 110.265
    potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] KCNA4 Low confidence 209.579 8.328 201.251
    305 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] HOMER1 Divided 210.05 1.04267 201.454
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B Subtracted High confidence 88.2482 22.0168 110.265
    mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 Divided 242.339 1.1017 266.986
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Subtracted Low confidence 200.288 8.284 192.004
    306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] no value Divided High confidence 242.153 1.10126 266.673
    cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] NUDT21 Subtracted Low confidence 212.262 8.271 203.991
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] no value High confidence 88.2482 22.0168 110.265
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Divided Low confidence 202.122 1.04258 193.867
    307 integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] ITGB1BP2 Subtracted 212.262 8.271 203.991
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] MAGEA6 High confidence 88.2482 22.0168 110.265
    phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816] PHKG1 Divided Low confidence 217.957 1.04245 227.209
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR High confidence 242.153 1.10126 266.673
    308 60s ribosomal protein l34. [swissprot;acc:p49207] RPL34
    homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] HOMER2 Low confidence 210.018 1.0424 201.475
    necdin. [swissprot;acc:q99608] NDN Subtracted High confidence 88.2482 22.0168 110.265
    rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] RAB3GAP2 Low confidence 212.262 8.271 203.991
    309 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] MAGED1 High confidence 88.2482 22.0168 110.265
    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 1.04222 192.103
    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 8.266 197.484
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Divided High confidence 242.153 1.10126 266.673
    310 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] MAGEF1 Subtracted 88.2482 22.0168 110.265
    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 1.04186 197.484
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 High confidence 242.153 1.10126 266.673
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Subtracted Low confidence 202.122 8.255 193.867
    311 exocyst complex component exo70. [swissprot;acc:q9upt5] EXOC7 204.124 8.215 212.339
    melanoma antigen, family b, 6. [refseq;acc:nm_173523] MAGEB6B High confidence 88.2482 22.0168 110.265
    protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B Divided 242.627 1.10108 267.151
    ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] UBE1C Low confidence 192.088 1.04184 184.374
    312 60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L High confidence 242.195 1.10103 266.663
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] no value Subtracted 88.2482 22.0168 110.265
    transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] BACH1 Low confidence 172.647 8.207 164.44
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] SNRPA1 Divided 202.051 1.04184 193.937
    313 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] no value 202.05 1.04182 193.94
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 Subtracted High confidence 88.2482 22.0168 110.265

    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/