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 [...,...].
    description Rank Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2075 to 2124 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 474 KCNA2 226.789 210.818 1.07576
    potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 476 KCNA4 226.681 210.814 1.07527
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 123 KCND1 269.23 327.601 1.21681
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 120 KCND2 269.278 327.709 1.21699
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] 122 KCND3 269.248 327.642 1.21688
    potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 718 CPXM1 223.121 211.685 1.05402
    potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 714 CPXM2
    potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] 1843 ATP11A 212.455 210.113 1.01115
    potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] 1820 ATP9A 220.462 217.926 1.01164
    pp1201 protein. [refseq;acc:nm_022152] 1627 TMBIM1 217.446 214.2 1.01515
    pp3111 protein. [refseq;acc:nm_022156] 236 DUS1L 227.357 254.15 1.11785
    pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 641 PRAM1 217.67 230.596 1.05938
    pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] 1787 PBX4 206.332 203.874 1.01206
    pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 1779 PBX1
    pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] 1786 no value
    pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] 1781 PBX3
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] 2635 CLP1 166.612 166.393 1.00132
    pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 1445 PCF11 134.233 136.922 1.02003
    pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] 1743 no value 218.176 215.402 1.01288
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 473 PRPF31 225.661 209.651 1.07637
    pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 594 CDC40 223.282 210.136 1.06256
    prefoldin subunit 1. [swissprot;acc:o60925] 1645 PFDN1 217.256 214.149 1.01451
    prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] 1310 PFDN2 226.439 221.26 1.02341
    prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 1309 VBP1
    prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4] 3130 PFDN4 0.00001 0.00001 1
    prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 977 PFDN5 228.953 221.421 1.03402
    prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] 978 no value
    preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 574 MOBKL3 221.807 208.264 1.06503
    presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 211 PSEN1 285.684 252.234 1.13261
    presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 207 PSEN2
    presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 3100 no value 0.00001 0.00001 1
    presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 736 232.601 244.534 1.0513
    presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 734
    presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 1841 PARL 212.455 210.113 1.01115
    presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] 2658 DLG4 216.933 216.7 1.00108
    presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796] 2659 DLG3
    presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] 2660 DLG1 216.937 216.704
    prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] 913 TGS1 210.863 218.878 1.03801
    prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5] 3143 PICK1 0.00001 0.00001 1
    probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 376 DDX56 257.017 234.945 1.09395
    probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] 2645 DHX35 194.097 194.328 1.00119
    probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] 1675 DDX20 228.496 231.729 1.01415
    probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 837 DDX6 231.734 222.222 1.0428
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 1097 ATP2C2 209.123 203.208 1.02911
    probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] 2266 ATP13A2 211.597 210.416 1.00561
    probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] 1321 DIMT1L 226.347 221.259 1.023
    probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 1221 PET112L 211.959 217.258 1.025
    probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 1737 LARS2 218.99 216.189 1.01296
    probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 1031 EMG1 242.978 235.518 1.03167
    probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 497 EBNA1BP2 251.344 234.514 1.07177

    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/