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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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measured Hugo Gene Rank expected final description
Results: HTML CSV LaTeX Showing element 2708 to 2757 of 3206 in total
measured
Hugo
Rank
expected
final
description
0.383948 C19orf29 2883 2.08123 0.184481292 NY-REN-24 ANTIGEN (FRAGMENT). [SPTREMBL;Acc:Q9Y5A4]
0.384181 BCAT2 1452 1.57878 0.243340427 "BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.6.1.42) (BCAT(M)) (PLACENTAL PROTEIN 18) (PP18). [SWISSPROT;Acc:O15382]"
0.384329 LGALS4 2466 1.77366 0.216686964 GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [SWISSPROT;Acc:P56470]
0.384939 ARF1 486 1.40333 0.274303977 ADP-RIBOSYLATION FACTOR 1. [SWISSPROT;Acc:P32889]
0.385887 ADSSL1 2178 1.7008 0.226885583 ADENYLOSUCCINATE SYNTHASE-LIKE 1. [RefSeq;Acc:NM_152328]
0.386694 LAMC1 839 1.48326 0.260705473 LAMININ GAMMA-1 CHAIN PRECURSOR (LAMININ B2 CHAIN). [SWISSPROT;Acc:P11047]
0.386793 CSTF2 2128 1.69586 0.228080738 "CLEAVAGE STIMULATION FACTOR, 64 KDA SUBUNIT (CSTF 64 KDA SUBUNIT) (CF-1 64 KDA SUBUNIT). [SWISSPROT;Acc:P33240]"
0.387487 CDIPT 2736 1.88714 0.205330288 CDP-DIACYLGLYCEROL--INOSITOL 3-PHOSPHATIDYLTRANSFERASE (EC 2.7.8.11) (PHOSPHATIDYLINOSITOL SYNTHASE) (PTDINS SYNTHASE) (PI SYNTHASE). [SWISSPROT;Acc:O14735]
0.388695 CSTF2T 2075 1.69606 0.229175265 LIKELY ORTHOLOG OF MOUSE VARIANT POLYADENYLATION PROTEIN CSTF-64. [RefSeq;Acc:NM_015235]
0.388823 SCYE1 2803 1.9597 0.19840945 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P43 [CONTAINS: ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II (EMAP-II) (SMALL INDUCIBLE CYTOKINE SUBFAMILY E MEMBER 1)]. [SWISSPROT;Acc:Q12904]
0.390142 no value 1487 1.60666 0.242827979 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM2 (SMALL NUCLEAR RIBONUCLEAR PROTEIN D HOMOLOG) (G7B) (SNRNP CORE SM-LIKE PROTEIN SM-X5). [SWISSPROT;Acc:Q9Y333]
0.390544 MEMO1P 2060 1.70053 0.229660165 PROTEIN CGI-27 (C21ORF19-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y316]
0.390781 ACTR2 729 1.47645 0.264676081 ACTIN-LIKE PROTEIN 2 (ACTIN-RELATED PROTEIN 2). [SWISSPROT;Acc:O15142]
0.391086 TAF6 2348 1.77434 0.220412097 TRANSCRIPTION INITIATION FACTOR TFIID 70 KDA SUBUNIT (TAFII-70) (TAFII-80) (TAFII80). [SWISSPROT;Acc:P49848]
0.391899 LIPT1 2121 1.71793 0.228122799 "LIPOATE-PROTEIN LIGASE, MITOCHONDRIAL PRECURSOR (EC 6.-.-.-) (LIPOATE BIOSYNTHESIS PROTEIN) (LIPOYL LIGASE) (LIPOYLTRANSFERASE). [SWISSPROT;Acc:Q9Y234]"
0.392337 PRKAR2A 1629 1.63914 0.239355394 CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY CHAIN. [SWISSPROT;Acc:P13861]
0.392968 ARPC3 725 1.48471 0.264676604 ARP2/3 COMPLEX 21 KDA SUBUNIT (P21-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 3). [SWISSPROT;Acc:O15145]
0.393043 PGM2L1 589 1.45917 0.269360664
0.393069 SOS1 124 1.09904 0.357647583 SON OF SEVENLESS PROTEIN HOMOLOG 1 (SOS-1). [SWISSPROT;Acc:Q07889]
0.394428 GUF1 1938 1.70248 0.231678493
0.394562 CBL 94 1.04353 0.378103169 CBL E3 UBIQUITIN PROTEIN LIGASE (EC 6.3.2.-) (SIGNAL TRANSDUCTION PROTEIN CBL) (PROTO-ONCOGENE C-CBL). [SWISSPROT;Acc:P22681]
0.39546 no value 647 1.47537 0.268041237 RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260]
0.396471 TAF12 2299 1.78321 0.222335563 TRANSCRIPTION INITIATION FACTOR TFIID 20/15 KDA SUBUNITS (TAFII- 20/TAFII-15) (TAFII20/TAFII15). [SWISSPROT;Acc:Q16514]
0.396527 ETFA 2778 1.97038 0.201243922 "ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT, MITOCHONDRIAL PRECURSOR (ALPHA-ETF). [SWISSPROT;Acc:P13804]"
0.397319 KYNU 2614 1.88014 0.211324157 KYNURENINASE (EC 3.7.1.3) (L-KYNURENINE HYDROLASE). [SWISSPROT;Acc:Q16719]
0.398002 ISL1 2724 1.93018 0.206199422 INSULIN GENE ENHANCER PROTEIN ISL-1 (ISLET-1). [SWISSPROT;Acc:P20663]
0.398407 no value 1060 1.57699 0.25263762 GERM CELL-LESS. [RefSeq;Acc:NM_022471]
0.398698 CTBP2 738 1.50657 0.264639545 C-TERMINAL BINDING PROTEIN 2 (CTBP2). [SWISSPROT;Acc:P56545]
0.398804 TFIP11 320 1.37218 0.290635339 TUFTELIN-INTERACTING PROTEIN 11 (HSPC006). [SWISSPROT;Acc:Q9UBB9]
0.399289 PSMD2 2164 1.75758 0.227181124 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 2 (26S PROTEASOME REGULATORY SUBUNIT S2) (26S PROTEASOME SUBUNIT P97) (TUMOR NECROSIS FACTOR TYPE 1 RECEPTOR ASSOCIATED PROTEIN 2) (55.11 PROTEIN). [SWISSPROT;Acc:Q13200]
0.401253 TIA1 111 1.10989 0.361525016 NUCLEOLYSIN TIA-1 (RNA-BINDING PROTEIN TIA-1) (P40-TIA-1) [CONTAINS: P15-TIA-1]. [SWISSPROT;Acc:P31483]
0.402903 ARPC5 717 1.52156 0.264795999 ARP2/3 COMPLEX 16 KDA SUBUNIT (P16-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 5). [SWISSPROT;Acc:O15511]
0.403209 VPS39 1896 1.73336 0.232616998 VAM6/VPS39-LIKE PROTEIN (HVAM6P). [SWISSPROT;Acc:Q96JC1]
0.403445 CMPK 1965 1.74487 0.231217798 UMP-CMP KINASE (EC 2.7.4.14) (CYTIDYLATE KINASE) (DEOXYCYTIDYLATE KINASE) (CYTIDINE MONOPHOSPHATE KINASE). [SWISSPROT;Acc:P30085]
0.403732 ARID4B 1373 1.64923 0.244800301
0.404169 FNBP1 409 1.45394 0.277981897 "BA138E2.1.2 (FORMIN-BINDING PROTEIN 17 (FBP17), ISOFORM 2). [SPTREMBL;Acc:Q96LH6]"
0.404388 FOXA1 580 1.49712 0.270110612 HEPATOCYTE NUCLEAR FACTOR 3-ALPHA (HNF-3A) (FORKHEAD BOX PROTEIN A1). [SWISSPROT;Acc:P55317]
0.404521 PRKAB2 241 1.29474 0.312434157 "5'-AMP-ACTIVATED PROTEIN KINASE, BETA-2 SUBUNIT (AMPK BETA-2 CHAIN). [SWISSPROT;Acc:O43741]"
0.404881 TNPO2 532 1.49189 0.271387971 "KARYOPHERIN BETA 2B, TRANSPORTIN; IMPORTIN 3. [RefSeq;Acc:NM_013433]"
0.405058 STAM 2111 1.77451 0.228264704 SIGNAL TRANSDUCING ADAPTOR MOLECULE 1; SIGNAL TRANSDUCING ADAPTOR MOLECULE. [RefSeq;Acc:NM_003473]
0.40611 ATG5 653 1.51635 0.267820754 AUTOPHAGY PROTEIN 5-LIKE (APG5-LIKE) (APOPTOSIS-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q9H1Y0]
0.40616 no value 160 1.16002 0.350131894 HUNTINGTIN-INTERACTING PROTEIN HYPA/FBP11 (FRAGMENT). [SPTREMBL;Acc:O75404]
0.407104 RAD51 1973 1.76144 0.231119993 DNA REPAIR PROTEIN RAD51 HOMOLOG 1 (HRAD51) (HSRAD51). [SWISSPROT;Acc:Q06609]
0.407912 CDA 1105 1.62535 0.250968714 CYTIDINE DEAMINASE (EC 3.5.4.5) (CYTIDINE AMINOHYDROLASE). [SWISSPROT;Acc:P32320]
0.408379 U2AF2 1436 1.67604 0.243657073 SPLICING FACTOR U2AF 65 KDA SUBUNIT (U2 AUXILIARY FACTOR 65 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT) (HU2AF(65)). [SWISSPROT;Acc:P26368]
0.408607 DCLK1 1432 1.67671 0.24369569 SERINE/THREONINE-PROTEIN KINASE DCAMKL1 (EC 2.7.1.-) (DOUBLECORTIN- LIKE AND CAM KINASE-LIKE 1). [SWISSPROT;Acc:O15075]
0.410038 no value 2325 1.84872 0.221795621 40S RIBOSOMAL PROTEIN SA (P40) (34/67 KDA LAMININ RECEPTOR) (COLON CARCINOMA LAMININ-BINDING PROTEIN) (NEM/1CHD4) (MULTIDRUG RESISTANCE- ASSOCIATED PROTEIN MGR1-AG). [SWISSPROT;Acc:P08865]
0.410279 LIN7C 1501 1.6901 0.242754275 LIN-7 HOMOLOG C; LIN-7 PROTEIN 3. [RefSeq;Acc:NM_018362]
0.410655 no value 1390 1.68007 0.244427316
0.411399 2716 1.98421 0.207336421

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/