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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Rank Gene description expected measured final Hugo
Results: HTML CSV LaTeX Showing element 2608 to 2657 of 3206 in total
Rank
description
expected
measured
final
Hugo
2608 "3-KETOACYL-COA THIOLASE, PEROXISOMAL PRECURSOR (EC 2.3.1.16) (BETA- KETOTHIOLASE) (ACETYL-COA ACYLTRANSFERASE) (PEROXISOMAL 3-OXOACYL- COA THIOLASE). [SWISSPROT;Acc:P09110]" 3.15431 0.668547 0.211947145 ACAA1
2609 "ACETYL-COENZYME A SYNTHETASE, CYTOPLASMIC (EC 6.2.1.1) (ACETATE--COA LIGASE) (ACYL-ACTIVATING ENZYME) (ACETYL-COA SYNTHETASE) (ACS) (ACECS). [SWISSPROT;Acc:Q9NR19]" 2.37915 0.503361 0.21157178 ACSS2
2610 "ACYL-COENZYME A OXIDASE 1, PEROXISOMAL (EC 1.3.3.6) (PALMITOYL-COA OXIDASE) (AOX). [SWISSPROT;Acc:Q15067]" 4.61324 0.974934 0.2113339 ACOX1
2611 TOPOISOMERASE (DNA) II BINDING PROTEIN. [RefSeq;Acc:NM_007027] 0.218331 0.0461407 0.211333709 TOPBP1
2612 "ATP SYNTHASE F CHAIN, MITOCHONDRIAL (EC 3.6.3.14). [SWISSPROT;Acc:P56134]" 0.122212 0.0258274 0.211332766 ATP5J2
2613 PROBABLE ATP-DEPENDENT HELICASE DDX35 (DEAH-BOX PROTEIN 35). [SWISSPROT;Acc:Q9H5Z1] DHX35
2614 KYNURENINASE (EC 3.7.1.3) (L-KYNURENINE HYDROLASE). [SWISSPROT;Acc:Q16719] 1.88014 0.397319 0.211324157 KYNU
2615 "EXPORTIN 1; EXPORTIN-1 (REQUIRED FOR CHROMOSOME REGION MAINTENANCE); EXPORTIN 1 (CRM1, YEAST, HOMOLOG); CRM1, YEAST, HOMOLOG. [RefSeq;Acc:NM_003400]" 0.75356 0.159172 0.211226711 XPO1
2616 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 3 (EC 2.7.1.-) (MAP KINASE KINASE 3) (MAPKK 3) (MAPK/ERK KINASE 3). [SWISSPROT;Acc:P46734] 0.605166 0.127536 0.210745481 MAP2K3
2617 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 6 (EC 2.7.1.-) (MAP KINASE KINASE 6) (MAPKK 6) (MAPK/ERK KINASE 6) (SAPKK3). [SWISSPROT;Acc:P52564] 0.679075 0.143053 0.210658617 MAP2K6
2618 "CLEAVAGE STIMULATION FACTOR SUBUNIT 3; CLEAVAGE STIMULATION FACTOR, 3' PRE-RNA, SUBUNIT 3, 77KD. [RefSeq;Acc:NM_001326]" 1.95716 0.412171 0.210596477 CSTF3
2619 ALCOHOL DEHYDROGENASE CLASS III CHI CHAIN (EC 1.1.1.1) (GLUTATHIONE- DEPENDENT FORMALDEHYDE DEHYDROGENASE) (EC 1.2.1.1) (FDH). [SWISSPROT;Acc:P11766] 2.27081 0.478004 0.210499337 no value
2620 ESTERASE D (EC 3.1.1.1). [SWISSPROT;Acc:P10768] 0.119364 0.025126 0.210498978 ESD
2621 RHO-GTPASE-ACTIVATING PROTEIN 7 (RHO-TYPE GTPASE-ACTIVATING PROTEIN 7) (DELETED IN LIVER CANCER 1 PROTEIN) (DLC-1) (HP PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 12) (STARD12) (START DOMAIN-CONTAINING PROTEIN 12). [SWISSPROT;Acc:Q96QB1] 0.115107 0.0241725 0.210000261 DLC1
2622 MITOGEN-ACTIVATED PROTEIN KINASE 12 (EC 2.7.1.37) (EXTRACELLULAR SIGNAL-REGULATED KINASE 6) (ERK-6) (ERK5) (STRESS-ACTIVATED PROTEIN KINASE-3) (MITOGEN-ACTIVATED PROTEIN KINASE P38 GAMMA) (MAP KINASE P38 GAMMA). [SWISSPROT;Acc:P53778] 0.157765 0.0331306 0.209999683 MAPK11
2623 SPHINGOSINE KINASE 1 (EC 2.7.1.-) (SK 1) (SPK 1). [SWISSPROT;Acc:Q9NYA1] 0.115136 0.0241785 0.209999479 SPHK1
2624 SPHINGOSINE KINASE 2 (EC 2.7.1.-) (SK 2) (SPK 2). [SWISSPROT;Acc:Q9NRA0] SPHK2
2625 STAR-RELATED LIPID TRANSFER PROTEIN 13 (STARD13) (START DOMAIN- CONTAINING PROTEIN 13) (46H23.2). [SWISSPROT;Acc:Q9Y3M8] 0.0938936 0.0197176 0.209999404 STARD13
2626 MITOGEN-ACTIVATED PROTEIN KINASE-ACTIVATED PROTEIN KINASE 3; MAPKAP KINASE 3. [RefSeq;Acc:NM_004635] 0.250939 0.052697 0.209999243 MAPKAPK3
2627 UDP-N-ACETYLGLUCOSAMINE--DOLICHYL-PHOSPHATE N- ACETYLGLUCOSAMINEPHOSPHOTRANSFERASE (EC 2.7.8.15) (GPT) (G1PT) (N-ACETYLGLUCOSAMINE-1-PHOSPHATE TRANSFERASE) (GLCNAC-1-P TRANSFERASE). [SWISSPROT;Acc:Q9H3H5] 0.326785 0.0686246 0.209999235 DPAGT1
2628 MITOGEN-ACTIVATED PROTEIN KINASE 14 (EC 2.7.1.37) (MITOGEN-ACTIVATED PROTEIN KINASE P38ALPHA) (MAP KINASE P38ALPHA) (CYTOKINE SUPPRESSIVE ANTI-INFLAMMATORY DRUG BINDING PROTEIN) (CSAID BINDING PROTEIN) (CSBP) (MAX-INTERACTING PROTEIN 2) (MAP KINASE MXI2) 0.206986 0.0434669 0.209999227 MAPK14
2629 MAP KINASE-ACTIVATED PROTEIN KINASE 2 (EC 2.7.1.-) (MAPK-ACTIVATED PROTEIN KINASE 2) (MAPKAP KINASE 2) (MAPKAPK-2). [SWISSPROT;Acc:P49137] 0.320798 0.0673673 0.209999127 MAPKAPK2
2630 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15822]" 0.0677865 0.0142351 0.209999041 CHRNA2
2631 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15825]" 0.0626341 0.0131531 0.209999026 CHRNA6
2632 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [SWISSPROT;Acc:P43681]" 0.0888852 0.0186658 0.209998965 CHRNA4
2633 STAR-RELATED LIPID TRANSFER PROTEIN 8 (STARD8) (START DOMAIN- CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q92502] 0.0901805 0.0189378 0.209998836 STARD8
2634 NITROGEN FIXATION CLUSTER-LIKE. [RefSeq;Acc:NM_014301] 1.98305 0.416438 0.209998739 ISCU
2635 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [SWISSPROT;Acc:P32297]" 0.0632961 0.0132921 0.20999872 CHRNA3
2636 TRANSFORMING PROTEIN RHOC (H9). [SWISSPROT;Acc:P08134] 0.102796 0.0215869 0.209997471 RHOC
2637 CYSTATHIONINE BETA-SYNTHASE (EC 4.2.1.22) (SERINE SULFHYDRASE) (BETA-THIONASE). [SWISSPROT;Acc:P35520] 1.25182 0.262879 0.209997444 CBS
2638 TRANSFORMING PROTEIN RHOA (H12). [SWISSPROT;Acc:P06749] 0.117481 0.0246707 0.209997361 RHOA
2639 3-MERCAPTOPYRUVATE SULFURTRANSFERASE (EC 2.8.1.2) (MST). [SWISSPROT;Acc:P25325] MPST
2640 AARSD1
2641 THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1) (RHODANESE). [SWISSPROT;Acc:Q16762] 0.10215 0.0214512 0.209997063 TST
2642 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 2) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 2) (CDP- DIACYLGLYCEROL SYNTHASE 2) (CDS 2) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2) (CDP-DAG SYNTHASE 2) (CDP-DG SYNTHETASE 2). [Source 2.45712 0.515928 0.209972651 CDS2
2643 TBC1 DOMAIN FAMILY MEMBER 5. [SWISSPROT;Acc:Q92609] 0.547991 0.115058 0.209963302 TBC1D5
2644 TUBBY PROTEIN HOMOLOG. [SWISSPROT;Acc:P50607] 0.427882 0.0898392 0.20996256 TUB
2645 "PROTEIN KINASE C, ZETA TYPE (EC 2.7.1.37) (NPKC-ZETA). [SWISSPROT;Acc:Q05513]" 0.335687 0.0704817 0.209962554 PRKCZ
2646 VACUOLAR PROTEIN SORTING 29 (VESICLE PROTEIN SORTING 29) (HVPS29) (MDS007) (PEP11) (DC7/DC15). [SWISSPROT;Acc:Q9UBQ0] 0.8539 0.179287 0.209962525 VPS29
2647 TUBBY RELATED PROTEIN 1 (TUBBY-LIKE PROTEIN 1). [SWISSPROT;Acc:O00294] 0.331879 0.0696821 0.209962366 TULP1
2648 "PROTEIN KINASE C, IOTA TYPE (EC 2.7.1.37) (NPKC-IOTA) (ATYPICAL PROTEIN KINASE C-LAMDA/IOTA) (APKC-LAMBDA/IOTA). [SWISSPROT;Acc:P41743]" 0.411431 0.086385 0.209962302 PRKCI
2649 PARTITIONING DEFECTIVE-6 HOMOLOG GAMMA (PAR-6 GAMMA) (PAR6D). [SWISSPROT;Acc:Q9BYG4] 0.239646 0.0503166 0.209962194 PARD6G
2650 VACUOLAR PROTEIN SORTING 35 (VESICLE PROTEIN SORTING 35) (HVPS35) (MATERNAL-EMBRYONIC 3). [SWISSPROT;Acc:Q96QK1] 0.152326 0.0319827 0.209962186 VPS35
2651 TUBBY RELATED PROTEIN 3 (TUBBY-LIKE PROTEIN 3). [SWISSPROT;Acc:O75386] 0.332641 0.069842 0.209962091 TULP3
2652 NUMB PROTEIN HOMOLOG (H-NUMB) (PROTEIN S171). [SWISSPROT;Acc:P49757] 0.619508 0.130073 0.209961776 NUMB
2653 NUMB-LIKE PROTEIN (NUMB-R). [SWISSPROT;Acc:Q9Y6R0] 0.584702 0.122765 0.209961656 NUMBL
2654 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828] 0.171181 0.0359383 0.209943276 SCAMP3
2655 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127] 0.174446 0.0366237 0.209942905 SCAMP2
2656 SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 1. [SWISSPROT;Acc:O15126] 0.221972 0.0466014 0.209942695 SCAMP1
2657 "SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]" 0.188319 0.0395353 0.209937924 SLC13A3

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/