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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Gene measured Hugo Rank description expected final
Results: HTML CSV LaTeX Showing element 2008 to 2057 of 3206 in total
measured
Hugo
Rank
description
expected
final
0.17249 CDK3 2899 CELL DIVISION PROTEIN KINASE 3 (EC 2.7.1.-). [SWISSPROT;Acc:Q00526] 0.985597 0.175010679
0.172887 REXO4 2490 XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] 0.801332 0.215749527
0.172935 LASS2 2922 LAG1 LONGEVITY ASSURANCE HOMOLOG 2 ISOFORM 1; L3 PIGMENT; TUMOR METASTASIS-SUPPRESSOR. [RefSeq;Acc:NM_022075] 1.02934 0.168005712
0.173246 GADD45B 47 GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 BETA (NEGATIVE GROWTH-REGULATORY PROTEIN MYD118) (MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD118). [SWISSPROT;Acc:O75293] 0.415438 0.417020109
0.173405 OGT 2105 UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT (EC 2.4.1.-) (O-GLCNAC TRANSFERASE P110 SUBUNIT). [SWISSPROT;Acc:O15294] 0.759373 0.228352865
0.173445 EIF4E 655 EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (EIF-4E) (EIF4E) (MRNA CAP-BINDING PROTEIN) (EIF-4F 25 KDA SUBUNIT). [SWISSPROT;Acc:P06730] 0.648176 0.267589358
0.173712 no value 2903 60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268] 0.997527 0.174142655
0.173881 PTPN2 453 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2 (EC 3.1.3.48) (T- CELL PROTEIN-TYROSINE PHOSPHATASE) (TCPTP). [SWISSPROT;Acc:P17706]" 0.6302 0.275913996
0.174044 GADD45A 48 GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 ALPHA (DNA- DAMAGE INDUCIBLE TRANSCRIPT 1) (DDIT1). [SWISSPROT;Acc:P24522] 0.417352 0.417019686
0.174535 GLUL 2564 GLUTAMINE SYNTHETASE (EC 6.3.1.2) (GLUTAMATE--AMMONIA LIGASE). [SWISSPROT;Acc:P15104] 0.8167 0.213707604
0.174557 no value 2902 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735] 0.999179 0.174700429
0.174649 YIPF5 947 GOLGI MEMBRANE PROTEIN SB140; SMOOTH MUSCLE CELL ASSOCIATED PROTEIN 5. [RefSeq;Acc:NM_030799] 0.681143 0.256405777
0.174683 HOMER2 3083 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 2; HOMER HOMOLOG 3 (DROSOPHILA). [RefSeq;Acc:NM_004839]" 1.74914 0.099867935
0.174876 RPP30 2264 RIBONUCLEASE P PROTEIN SUBUNIT P30 (EC 3.1.26.5) (RNASEP PROTEIN P30) (RNASE P SUBUNIT 2). [SWISSPROT;Acc:P78346] 0.784403 0.222941524
0.174979 AZIN1 2504 ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [SWISSPROT;Acc:O14977] 0.814661 0.214787501
0.175357 ENOPH1 2451 E-1 ENZYME. [RefSeq;Acc:NM_021204] 0.808504 0.216890702
HDHD3 2450
0.175549 LMNA 1592 LAMIN A/C (70 KDA LAMIN). [SWISSPROT;Acc:P02545] 0.730667 0.240258558
0.175589 RTN2 2685 RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [SWISSPROT;Acc:O75298] 0.842838 0.208330664
0.175846 ESRRB 2706 "STEROID HORMONE RECEPTOR ERR2 (ESTROGEN-RELATED RECEPTOR, BETA) (ERR-BETA) (ESTROGEN RECEPTOR-LIKE 2) (ERR BETA-2). [SWISSPROT;Acc:O95718]" 0.847805 0.207413261
0.176025 KHDRBS1 150 "KH DOMAIN CONTAINING, RNA BINDING, SIGNAL TRANSDUCTION ASSOCIATED 1; GAP-ASSOCIATED TYROSINE PHOSPHOPROTEIN P62 (SAM68). [RefSeq;Acc:NM_006559]" 0.501115 0.351266675
0.176498 THOC7 323 0.613112 0.287872363
0.176631 PEO1 861 TWINKLE; LIKELY ORTHOLOG OF MOUSE T7 GP4-LIKE PROTEIN WITH INTRAMITOCHONDRIAL NUCLEOID LOCALIZATION. [RefSeq;Acc:NM_021830] 0.678587 0.260292343
0.176971 RPL15 2249 60S RIBOSOMAL PROTEIN L15. [SWISSPROT;Acc:P39030] 0.792735 0.223241058
0.176985 BCKDHB 432 "2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN) (BCKDH E1-BETA). [SWISSPROT;Acc:P21953]" 0.63809 0.277366829
CNOT4 430 "CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 4; NOT4 (NEGATIVE REGULATOR OF TRANSCRIPTION 4, YEAST) HOMOLOG; CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT. [RefSeq;Acc:NM_013316]"
PTBP1 433 POLYPYRIMIDINE TRACT-BINDING PROTEIN 1 (PTB) (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN I) (HNRNP I) (57 KDA RNA-BINDING PROTEIN PPTB-1). [SWISSPROT;Acc:P26599]
RC3H2 434 MEMBRANE-ASSOCIATED NUCLEIC ACID BINDING PROTEIN. [RefSeq;Acc:NM_018835]
RERE 431 ARGININE-GLUTAMIC ACID DIPEPTIDE (RE) REPEATS; ATROPHIN 1-LIKE; ARGININE GLUTAMIC ACID DIPEPTIDE RE REPEATS. [RefSeq;Acc:NM_012102]
SALL1 429 SAL-LIKE PROTEIN 1 (ZINC FINGER PROTEIN SALL1) (SPALT-LIKE TRANSCRIPTION FACTOR 1) (HSAL1). [SWISSPROT;Acc:Q9NSC2]
0.177169 PRKAG3 243 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-3 SUBUNIT (AMPK GAMMA-3 CHAIN) (AMPK GAMMA3). [SWISSPROT;Acc:Q9UGI9]" 0.567061 0.312433759
0.177185 PARL 1080 PRESENILINS ASSOCIATED RHOMBOID-LIKE PROTEIN. [RefSeq;Acc:NM_018622] 0.702909 0.252073882
0.177407 RPL30 1971 60S RIBOSOMAL PROTEIN L30. [SWISSPROT;Acc:P04645] 0.767511 0.231145873
0.177425 MDH2 2926 "MALATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.1.37). [SWISSPROT;Acc:P40926]" 1.08227 0.163937834
0.177598 SOLH 1079 "SMALL OPTIC LOBES HOMOLOG; SMALL OPTIC LOBES, DROSOPHILA, HOMOLOG OF. [RefSeq;Acc:NM_005632]" 0.704023 0.252261645
0.177719 ADC 2505 ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [SWISSPROT;Acc:Q96A70] 0.827431 0.214784073
0.177815 PLD1 2429 PHOSPHOLIPASE D1 (EC 3.1.4.4) (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (HPLD1). [SWISSPROT;Acc:Q13393] 0.816721 0.217718168
0.177901 DTX1 147 DELTEX HOMOLOG 1; HDX-1. [RefSeq;Acc:NM_004416] 0.506388 0.351313617
0.178008 WASF3 704 WISKOTT-ALDRICH SYNDROME PROTEIN FAMILY MEMBER 3 (WASP-FAMILY PROTEIN MEMBER 3) (VERPROLIN HOMOLOGY DOMAIN-CONTAINING PROTEIN 3). [SWISSPROT;Acc:Q9UPY6] 0.671355 0.265147351
0.178897 TBC1D10B 1022 0.705791 0.25347022
0.179057 TOM1L2 774 TARGET OF MYB1-LIKE 2; TARGET OF MYB1 (CHICKEN) HOMOLOG-LIKE 2. [RefSeq;Acc:NM_144678] 0.680239 0.263226601
0.179279 HPCAL1 1221 VISININ-LIKE PROTEIN 3 (VILIP-3) (CALCIUM-BINDING PROTEIN BDR-1) (HLP2) (HIPPOCALCIN-LIKE PROTEIN 1). [SWISSPROT;Acc:P37235] 0.722847 0.248017907
0.179287 VPS29 2646 VACUOLAR PROTEIN SORTING 29 (VESICLE PROTEIN SORTING 29) (HVPS29) (MDS007) (PEP11) (DC7/DC15). [SWISSPROT;Acc:Q9UBQ0] 0.8539 0.209962525
0.179445 HNRPH3 366 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN H3 (HNRNP H3) (HNRNP 2H9). [SWISSPROT;Acc:P31942] 0.641462 0.279743773
0.179673 PPP1R8 1665 "NUCLEAR INHIBITOR OF PROTEIN PHOSPHATASE-1 (NIPP-1) (PROTEIN PHOSPHATASE 1, REGULATORY INHIBITOR SUBUNIT 8) [INCLUDES: ACTIVATOR OF RNA DECAY (EC 3.1.4.-) (ARD-1)]. [SWISSPROT;Acc:Q12972]" 0.752395 0.238801427
0.179735 TARSL2 2780 0.894194 0.201002243
0.180241 RAD54L 1735 RAD54-LIKE PROTEIN; RAD54 HOMOLOG. [RefSeq;Acc:NM_003579] 0.760447 0.237019805
0.180388 no value 2097 URIDINE KINASE-LIKE 1. [SWISSPROT;Acc:Q9NWZ5] 0.789739 0.228414704
0.180475 PRKAG1 242 "5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT (AMPK GAMMA-1 CHAIN) (AMPKG). [SWISSPROT;Acc:P54619]" 0.577642 0.312433999
0.180926 APOA1BP 2284 APOLIPOPROTEIN A-I BINDING PROTEIN; APOA-I BINDING PROTEIN. [RefSeq;Acc:NM_144772] 0.813521 0.222398684

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/