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