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 Value Type Network Comparison Type red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 880 to 929 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		Interaction Map
    		green
    		network_comparison
    440 NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 231.802 High confidence 249.983 1.07843
    441 CYP4B1 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 203.045 Low confidence 196.204 1.03487
    GRAP grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 High confidence 207.222 1.07835
    442 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 201.424 Low confidence 194.652 1.03479
    ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 High confidence 207.55 1.0783
    443 no value huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 201.418 Low confidence 194.664 1.0347
    NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 223.79 High confidence 207.539 1.0783
    444 NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 223.801 207.549
    PRPF6 u5 snrnp-associated 102 kda protein (u5-102 kda protein). [swissprot;acc:o94906] 207.002 Low confidence 200.066 1.03467
    445 NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 223.801 High confidence 207.549 1.0783
    UTP14A serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] 206.703 Low confidence 199.782 1.03464
    446 GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 224.049 High confidence 207.785 1.07827
    JMJD2B f16601_1, partial cds (fragment). [sptrembl;acc:o75274] 206.703 Low confidence 199.782 1.03464
    447 JMJD2C gene amplified in squamous cell carcinoma 1. [refseq;acc:nm_015061]
    NEK2 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] 224.049 High confidence 207.785 1.07827
    448 CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] 203.074 Low confidence 196.277 1.03463
    MACF1 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 228.468 High confidence 246.338 1.07822
    449 CYP4A11 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 203.077 Low confidence 196.283 1.03461
    DST bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 228.463 High confidence 246.33 1.07821
    450 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 207.786 Low confidence 200.839 1.03459
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.94 High confidence 218.837 1.07815
    451 LIMCH1 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] 210.594 Low confidence 203.561 1.03455
    POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 239.092 High confidence 257.705 1.07785
    452 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 207.972 1.07784
    PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 202.01 Low confidence 195.266 1.03454
    453 C19orf29 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] 210.727 203.693 1.03453
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 224.161 High confidence 207.972 1.07784
    454 no value 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
    CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 210.252 Low confidence 203.24 1.0345
    455 CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 210.251 203.241 1.03449
    TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 210.225 High confidence 226.578 1.07779
    456 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
    CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 210.251 Low confidence 203.241 1.03449
    457 CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]
    UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] 210.225 High confidence 226.578 1.07779
    458 AP1B1 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] 206.948 Low confidence 200.058 1.03444
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.922 High confidence 218.925 1.07764
    459 BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 233.529 216.737 1.07748
    GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 207.797 Low confidence 214.954 1.03444
    460 no value proactivator polypeptide precursor [contains: saposin a (protein a); saposin b (sphingolipid activator protein 1) (sap-1) (cerebroside sulfate activator) (csact) (dispersin) (sulfatide/gm1 activator); saposin c (co-beta-glucosidase) (a1 activator) (glucosylceramidase activator) (sphingolipid activator protein 2) (sap-2); saposin d (protein c) (component c)]. [swissprot;acc:p07602] 209.188 202.243 1.03434
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 223.648 High confidence 207.62 1.0772
    461 KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] 201.429 Low confidence 194.776 1.03416
    462 MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] 254.434 High confidence 236.224 1.07709
    SLC7A5 large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650] 201.466 Low confidence 194.819 1.03412
    463 POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 238.921 High confidence 257.327 1.07704
    PRRX1 paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [swissprot;acc:p54821] 194.41 Low confidence 201.036 1.03408
    464 ELL2 rna polymerase ii elongation factor ell2. [swissprot;acc:o00472] 198.618 205.369 1.03399
    FNBP1 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 High confidence 226.764 1.07686
    465 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 248.152 267.226

    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/