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 expected Rank description measured Hugo final
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 3206 in total
expected
Rank
description
measured
Hugo
final
0.297931 2494 METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [SWISSPROT;Acc:P56192] 0.0641898 MARS 0.2154519
0.298003 3047 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 SUBUNIT. [SWISSPROT;Acc:P30670] 0.0317927 GNG5 0.106685839
0.298119 842 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-7 CHAIN PRECURSOR. [SWISSPROT;Acc:P36544]" 0.077721 CHRNA7 0.260704618
0.29839 1170 HEPATOCELLULAR CARCINOMA SUSCEPTIBILITY PROTEIN; X 003 PROTEIN; HDCMC29P; HSPC260; LIKELY ORTHOLOG OF MOUSE CD40 LIGAND-ACTIVATED SPECIFIC TRANSCRIPT 3 (CLAST3). [RefSeq;Acc:NM_020232] 0.0744175 TNFSF5IP1 0.249396763
0.29844 888 EXOCYST COMPLEX COMPONENT SEC3 (BM-012). [SWISSPROT;Acc:Q9NV70] 0.0775579 EXOC1 0.259877697
0.29864 607 LANTHIONINE SYNTHETASE C-LIKE PROTEIN 1; G PROTEIN-COUPLED RECEPTOR 69A; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT C)-LIKE 1; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT). [RefSeq;Acc:NM_006055] 0.0803201 LANCL1 0.26895292
0.298726 908 SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 16. [RefSeq;Acc:NM_006649] 0.0771492 UTP14A 0.258260747
0.299686 2095 SYMPLEKIN. [SWISSPROT;Acc:Q92797] 0.0685085 SYMPK 0.228600936
0.299985 2605 "HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:P54868]" 0.0635814 HMGCS2 0.211948597
0.300389 3046 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-8 SUBUNIT (GAMMA-9). [SWISSPROT;Acc:Q9UK08] 0.032048 GNG8 0.106688327
0.301176 2569 HISTONE DEACETYLASE 4 (HD4). [SWISSPROT;Acc:P56524] 0.0642768 HDAC4 0.213419396
0.301896 1640 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911] 0.0721691 ZFHX3 0.239052853
0.302004 1475 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 0.0733796 no value 0.24297559
0.302084 2980 HOMEOBOX PROTEIN HOX-A5 (HOX-1C). [SWISSPROT;Acc:P20719] 0.0421586 HOXA5 0.139559195
0.302153 2267 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] 0.0673124 POLS 0.222775878
0.30217 182 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-3 (ACTIVATING TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P18847] 0.101196 ATF3 0.334897574
0.302259 1620 SENESCENCE MARKER PROTEIN-30 (SMP-30) (REGUCALCIN) (RC). [SWISSPROT;Acc:Q15493] 0.0724203 RGN 0.239596836
0.302313 1595 CENTAURIN BETA 2 (CNT-B2). [SWISSPROT;Acc:Q15057] 0.0726324 CENTB2 0.240255629
0.302577 2153 STEROL REGULATORY ELEMENT BINDING PROTEIN-1 (SREBP-1) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:P36956] 0.0687827 SREBF1 0.227322962
0.302799 1335 SUPPRESSOR OF SWI4 1 HOMOLOG (SSF-1) (PETER PAN HOMOLOG). [SWISSPROT;Acc:Q9NQ55] 0.0742746 PPAN-P2RY11 0.245293412
0.303151 1412 RNA-BINDING PROTEIN 5 (RNA BINDING MOTIF PROTEIN 5) (PUTATIVE TUMOR SUPPRESSOR LUCA15) (G15 PROTEIN). [SWISSPROT;Acc:P52756] 0.0739703 RBM5 0.244004803
0.303444 2584 "RHESUS BLOOD GROUP, B GLYCOPROTEIN; RH TYPE B GLYCOPROTEIN. [RefSeq;Acc:NM_020407]" 0.0646696 RHBG 0.21311873
0.303457 1108 DNA DAMAGE BINDING PROTEIN 1 (DAMAGE-SPECIFIC DNA BINDING PROTEIN 1) (DDB P127 SUBUNIT) (DDBA) (UV-DAMAGED DNA-BINDING PROTEIN 1) (UV-DDB 1) (XERODERMA PIGMENTOSUM GROUP E COMPLEMENTING PROTEIN) (XPCE) (X- ASSOCIATED PROTEIN 1) (XAP-1). [SWISSPROT; 0.0761267 DDB1 0.250864867
0.303687 2339 "6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" 0.0670488 PGD 0.220782582
0.30421 88 APICAL-LIKE PROTEIN (APXL PROTEIN). [SWISSPROT;Acc:Q13796] 0.117195 SHROOM2 0.385243746
0.305551 387 "GRPE PROTEIN HOMOLOG 1, MITOCHONDRIAL PRECURSOR (MT-GRPE#1) (HMGE). [SWISSPROT;Acc:Q9HAV7]" 0.0851715 GRPEL1 0.278747247
0.305581 854 KINESIN-LIKE PROTEIN KIF13A (KINESIN-LIKE PROTEIN RBKIN). [SWISSPROT;Acc:Q9H1H9] 0.0796144 KIF13A 0.260534523
0.305803 1399 0.0746708 LSG1 0.244179423
0.305823 958 0.0783783 TIMM50 0.256286479
0.305877 1655 APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] 0.0730689 APEX2 0.238883277
0.30593 2857 TRNA (5-METHYLAMINOMETHYL-2-THIOURIDYLATE)-METHYLTRANSFERASE (EC 2.1.1.61). [SWISSPROT;Acc:O75648] 0.0583389 TRMU 0.190693623
0.306454 3045 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-3 SUBUNIT. [SWISSPROT;Acc:P29798] 0.0326969 GNG3 0.106694316
0.306494 685 HISTIDINE AMMONIA-LYASE (EC 4.3.1.3) (HISTIDASE). [SWISSPROT;Acc:P42357] 0.0814182 HAL 0.265643699
686 RIBOSOMAL PROTEIN S6 KINASE ALPHA 1 (EC 2.7.1.37) (S6K-ALPHA 1) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 1) (P90-RSK 1) (RIBOSOMAL S6 KINASE 1) (RSK-1) (PP90RSK1). [SWISSPROT;Acc:Q15418] RPS6KA1
687 SIPA1L2
0.307503 3027 T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808] 0.0365656 DYNLT3 0.11891136
0.307647 3044 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-4 SUBUNIT. [SWISSPROT;Acc:P50150] 0.0328245 GNG4 0.106695336
0.309407 1298 0.0760628 no value 0.245834128
0.309963 223 XENOTROPIC AND POLYTROPIC RETROVIRUS RECEPTOR. [RefSeq;Acc:NM_004736] 0.0985042 XPR1 0.317793414
0.309975 1467 "COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.3) (COPROPORPHYRINOGENASE) (COPROGEN OXIDASE) (COX). [SWISSPROT;Acc:P36551]" 0.0753291 CPOX 0.243016695
0.310798 1304 RAD9 HOMOLOG; CELL CYCLE CHECKPOINT CONTROL PROTEIN; RAD9 HOMOLOG (S. POMBE). [RefSeq;Acc:NM_004584] 0.0763771 RAD9A 0.245745146
0.311034 195 MAX INTERACTING PROTEIN 1 (MXI1 PROTEIN). [SWISSPROT;Acc:P50539] 0.10032 MXI1 0.322537086
0.311107 2843 AQUAPORIN 4 (WCH4) (MERCURIAL-INSENSITIVE WATER CHANNEL) (MIWC). [SWISSPROT;Acc:P55087] 0.0599642 AQP4 0.192744618
0.311645 665 PROLIFERATION-ASSOCIATED PROTEIN 2G4 (CELL CYCLE PROTEIN P38-2G4 HOMOLOG) (HG4-1). [SWISSPROT;Acc:Q9UQ80] 0.083217 PA2G4 0.26702498
0.311942 2793 STROMAL INTERACTION MOLECULE 1 PRECURSOR. [SWISSPROT;Acc:Q13586] 0.0623579 STIM1 0.199902225
2794 "ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.3) (MCAD). [SWISSPROT;Acc:P11310]" ACADM
0.312352 1557 0.0753661 no value 0.241285793
0.313678 2842 AQUAPORIN 5. [SWISSPROT;Acc:P55064] 0.0604602 AQP5 0.192746064
0.313795 228 NY-REN-62 ANTIGEN (FRAGMENT). [SPTREMBL;Acc:Q9Y590] 0.099292 KIF21A 0.316423142
0.314025 1015 INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3] 0.079717 no value 0.253855585

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/