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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expected Gene Rank measured description final Hugo
Results: HTML CSV LaTeX Showing element 1002 to 1051 of 3206 in total
expected
Rank
measured
description
final
Hugo
0.298003 3047 0.0317927 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 SUBUNIT. [SWISSPROT;Acc:P30670] 0.106685839 GNG5
0.298119 842 0.077721 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-7 CHAIN PRECURSOR. [SWISSPROT;Acc:P36544]" 0.260704618 CHRNA7
0.29839 1170 0.0744175 HEPATOCELLULAR CARCINOMA SUSCEPTIBILITY PROTEIN; X 003 PROTEIN; HDCMC29P; HSPC260; LIKELY ORTHOLOG OF MOUSE CD40 LIGAND-ACTIVATED SPECIFIC TRANSCRIPT 3 (CLAST3). [RefSeq;Acc:NM_020232] 0.249396763 TNFSF5IP1
0.29844 888 0.0775579 EXOCYST COMPLEX COMPONENT SEC3 (BM-012). [SWISSPROT;Acc:Q9NV70] 0.259877697 EXOC1
0.29864 607 0.0803201 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] 0.26895292 LANCL1
0.298726 908 0.0771492 SEROLOGICALLY DEFINED COLON CANCER ANTIGEN 16. [RefSeq;Acc:NM_006649] 0.258260747 UTP14A
0.299686 2095 0.0685085 SYMPLEKIN. [SWISSPROT;Acc:Q92797] 0.228600936 SYMPK
0.299985 2605 0.0635814 "HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 2.3.3.10) (HMG-COA SYNTHASE) (3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE). [SWISSPROT;Acc:P54868]" 0.211948597 HMGCS2
0.300389 3046 0.032048 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-8 SUBUNIT (GAMMA-9). [SWISSPROT;Acc:Q9UK08] 0.106688327 GNG8
0.301176 2569 0.0642768 HISTONE DEACETYLASE 4 (HD4). [SWISSPROT;Acc:P56524] 0.213419396 HDAC4
0.301896 1640 0.0721691 ALPHA-FETOPROTEIN ENHANCER BINDING PROTEIN (AT MOTIF-BINDING FACTOR) (AT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:Q15911] 0.239052853 ZFHX3
0.302004 1475 0.0733796 RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 0.24297559 no value
0.302084 2980 0.0421586 HOMEOBOX PROTEIN HOX-A5 (HOX-1C). [SWISSPROT;Acc:P20719] 0.139559195 HOXA5
0.302153 2267 0.0673124 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] 0.222775878 POLS
0.30217 182 0.101196 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-3 (ACTIVATING TRANSCRIPTION FACTOR 3). [SWISSPROT;Acc:P18847] 0.334897574 ATF3
0.302259 1620 0.0724203 SENESCENCE MARKER PROTEIN-30 (SMP-30) (REGUCALCIN) (RC). [SWISSPROT;Acc:Q15493] 0.239596836 RGN
0.302313 1595 0.0726324 CENTAURIN BETA 2 (CNT-B2). [SWISSPROT;Acc:Q15057] 0.240255629 CENTB2
0.302577 2153 0.0687827 STEROL REGULATORY ELEMENT BINDING PROTEIN-1 (SREBP-1) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 1). [SWISSPROT;Acc:P36956] 0.227322962 SREBF1
0.302799 1335 0.0742746 SUPPRESSOR OF SWI4 1 HOMOLOG (SSF-1) (PETER PAN HOMOLOG). [SWISSPROT;Acc:Q9NQ55] 0.245293412 PPAN-P2RY11
0.303151 1412 0.0739703 RNA-BINDING PROTEIN 5 (RNA BINDING MOTIF PROTEIN 5) (PUTATIVE TUMOR SUPPRESSOR LUCA15) (G15 PROTEIN). [SWISSPROT;Acc:P52756] 0.244004803 RBM5
0.303444 2584 0.0646696 "RHESUS BLOOD GROUP, B GLYCOPROTEIN; RH TYPE B GLYCOPROTEIN. [RefSeq;Acc:NM_020407]" 0.21311873 RHBG
0.303457 1108 0.0761267 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; 0.250864867 DDB1
0.303687 2339 0.0670488 "6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" 0.220782582 PGD
0.30421 88 0.117195 APICAL-LIKE PROTEIN (APXL PROTEIN). [SWISSPROT;Acc:Q13796] 0.385243746 SHROOM2
0.305551 387 0.0851715 "GRPE PROTEIN HOMOLOG 1, MITOCHONDRIAL PRECURSOR (MT-GRPE#1) (HMGE). [SWISSPROT;Acc:Q9HAV7]" 0.278747247 GRPEL1
0.305581 854 0.0796144 KINESIN-LIKE PROTEIN KIF13A (KINESIN-LIKE PROTEIN RBKIN). [SWISSPROT;Acc:Q9H1H9] 0.260534523 KIF13A
0.305803 1399 0.0746708 0.244179423 LSG1
0.305823 958 0.0783783 0.256286479 TIMM50
0.305877 1655 0.0730689 APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [RefSeq;Acc:NM_014481] 0.238883277 APEX2
0.30593 2857 0.0583389 TRNA (5-METHYLAMINOMETHYL-2-THIOURIDYLATE)-METHYLTRANSFERASE (EC 2.1.1.61). [SWISSPROT;Acc:O75648] 0.190693623 TRMU
0.306454 3045 0.0326969 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-3 SUBUNIT. [SWISSPROT;Acc:P29798] 0.106694316 GNG3
0.306494 685 0.0814182 HISTIDINE AMMONIA-LYASE (EC 4.3.1.3) (HISTIDASE). [SWISSPROT;Acc:P42357] 0.265643699 HAL
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 0.0365656 T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808] 0.11891136 DYNLT3
0.307647 3044 0.0328245 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-4 SUBUNIT. [SWISSPROT;Acc:P50150] 0.106695336 GNG4
0.309407 1298 0.0760628 0.245834128 no value
0.309963 223 0.0985042 XENOTROPIC AND POLYTROPIC RETROVIRUS RECEPTOR. [RefSeq;Acc:NM_004736] 0.317793414 XPR1
0.309975 1467 0.0753291 "COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.3) (COPROPORPHYRINOGENASE) (COPROGEN OXIDASE) (COX). [SWISSPROT;Acc:P36551]" 0.243016695 CPOX
0.310798 1304 0.0763771 RAD9 HOMOLOG; CELL CYCLE CHECKPOINT CONTROL PROTEIN; RAD9 HOMOLOG (S. POMBE). [RefSeq;Acc:NM_004584] 0.245745146 RAD9A
0.311034 195 0.10032 MAX INTERACTING PROTEIN 1 (MXI1 PROTEIN). [SWISSPROT;Acc:P50539] 0.322537086 MXI1
0.311107 2843 0.0599642 AQUAPORIN 4 (WCH4) (MERCURIAL-INSENSITIVE WATER CHANNEL) (MIWC). [SWISSPROT;Acc:P55087] 0.192744618 AQP4
0.311645 665 0.083217 PROLIFERATION-ASSOCIATED PROTEIN 2G4 (CELL CYCLE PROTEIN P38-2G4 HOMOLOG) (HG4-1). [SWISSPROT;Acc:Q9UQ80] 0.26702498 PA2G4
0.311942 2793 0.0623579 STROMAL INTERACTION MOLECULE 1 PRECURSOR. [SWISSPROT;Acc:Q13586] 0.199902225 STIM1
2794 "ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN SPECIFIC, MITOCHONDRIAL PRECURSOR (EC 1.3.99.3) (MCAD). [SWISSPROT;Acc:P11310]" ACADM
0.312352 1557 0.0753661 0.241285793 no value
0.313678 2842 0.0604602 AQUAPORIN 5. [SWISSPROT;Acc:P55064] 0.192746064 AQP5
0.313795 228 0.099292 NY-REN-62 ANTIGEN (FRAGMENT). [SPTREMBL;Acc:Q9Y590] 0.316423142 KIF21A
0.314025 1015 0.079717 INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q9NZM3] 0.253855585 no value
0.314027 20 0.149206 NEURON NAVIGATOR 1; NEURON NAVIGATOR-1; PORE MEMBRANE AND/OR FILAMENT INTERACTING LIKE PROTEIN 3. [RefSeq;Acc:NM_020443] 0.475137488 NAV1

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/