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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1725 to 1774 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
863 CSNK2A1P casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] High confidence 240.194 230.957 1.03999
NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Low confidence 202.981 197.889 1.02573
864 CSNK2A2 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] High confidence 240.194 230.957 1.03999
SLC16A6 monocarboxylate transporter 7 (mct 7) (mct 6). [swissprot;acc:o15403] Low confidence 200.605 195.573 1.02573
865 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] High confidence 211.961 203.814 1.03997
G3BP2 ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Low confidence 210.933 216.358 1.02572
866 GPSM2 mosaic protein lgn. [swissprot;acc:p81274] 207.56 202.355
SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] High confidence 221.306 212.806 1.03994
867 no value 40s ribosomal protein s3a. [swissprot;acc:p49241] 225.689 234.674 1.03981
EIF3D eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Low confidence 205.551 200.398 1.02571
868 COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 204.037 198.928 1.02568
MVD diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] High confidence 233.298 242.571 1.03975
869 EXOC4 exocyst complex component sec8. [swissprot;acc:q96a65] 217.762 209.449 1.03969
ZNHIT4 pap-1 binding protein. [refseq;acc:nm_031288] Low confidence 213.16 218.629 1.02566
870 no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] High confidence 211.908 203.832 1.03962
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Low confidence 208.623 213.975 1.02565
871 CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] High confidence 110.2 114.552 1.03949
HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Low confidence 191.561 186.777 1.02561
872 HNRPK heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] High confidence 224.413 233.272 1.03948
NDUFA5 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] Low confidence 203.141 198.068 1.02561
873 PRPF4 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] High confidence 224.413 233.272 1.03948
PTPMT1 nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489] Low confidence 203.141 198.068 1.02561
874 EIF3E eukaryotic translation initiation factor 3 subunit 6 (eif-3 p48) (eif3e) (mammary tumor-associated protein int-6) (viral integration site protein int-6). [swissprot;acc:q64252]
PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] High confidence 212.002 203.954 1.03946
875 BDP1 transcription factor-like nuclear regulator; putative transcription regulation nuclear protein; putative transcription factor-like nuclear regulator; tata box binding protein (tbp)-associated factor, rna polymerase iii, gtf3b subunit 1; b''90 component. [refseq;acc:nm_018429] Low confidence 203.139 198.068 1.0256
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] High confidence 212.002 203.954 1.03946
876 BBOX1 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Low confidence 203.744 198.658 1.0256
PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] High confidence 212.002 203.954 1.03946
877 DHX35 probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Low confidence 205.571 200.44 1.0256
PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] High confidence 212.002 203.954 1.03946
878 ATP11A potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Low confidence 203.744 198.658 1.0256
PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] High confidence 212.002 203.954 1.03946
879 no value 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Low confidence 203.354 198.284 1.02557
PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] High confidence 212.002 203.954 1.03946
880 PRKAG2 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Low confidence 201.49 196.469 1.02556
881 MAX max protein. [swissprot;acc:p25912] 204.973 199.865
MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] High confidence 227.604 219.001 1.03928
882 MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] 227.601 219.008 1.03924
STX1A syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Low confidence 210.979 205.723 1.02555
883 no value nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483] 202.572 197.533 1.02551
GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] High confidence 227.596 219.017 1.03917
884 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]
NDUFA4L2 nadh:ubiquinone oxidoreductase mlrq subunit homolog (nuoms). [swissprot;acc:q9nrx3] Low confidence 202.572 197.533 1.02551
885 CDC5L cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]
NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] High confidence 227.596 219.017 1.03917
886 ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018
LIG4 dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917] Low confidence 202.568 197.535 1.02548
887 EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 202.277 197.255 1.02546
TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] High confidence 244.155 234.96 1.03913

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/