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 Hugo description final
Results: HTML CSV LaTeX Showing element 1552 to 1601 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.504965 567 0.136702 DHRS7B 0.270715792
0.505165 82 0.198685 E2F1 TRANSCRIPTION FACTOR E2F1 (E2F-1) (RETINOBLASTOMA BINDING PROTEIN 3) (RBBP-3) (PRB-BINDING PROTEIN E2F-1) (PBR3) (RETINOBLASTOMA-ASSOCIATED PROTEIN 1) (RBAP-1). [SWISSPROT;Acc:Q01094] 0.393307137
0.505621 2032 0.116403 no value 0.23021789
0.506093 113 0.182783 ARID1A "SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1 (SWI-SNF COMPLEX PROTEIN P270) (B120). [SWISSPROT;Acc:O14497]" 0.361164845
114 PDCD6 PROGRAMMED CELL DEATH PROTEIN 6 (PROBABLE CALCIUM-BINDING PROTEIN ALG- 2). [SWISSPROT;Acc:O75340]
0.506251 1038 0.128252 RBL1 RETINOBLASTOMA-LIKE PROTEIN 1 (107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB1) (P107). [SWISSPROT;Acc:P28749] 0.253336784
0.5063 889 0.131576 KIF5A NEURONAL KINESIN HEAVY CHAIN (NKHC) (KINESIN HEAVY CHAIN ISOFORM 5A) (KINESIN HEAVY CHAIN NEURON-SPECIFIC 1). [SWISSPROT;Acc:Q12840] 0.259877543
0.506388 147 0.177901 DTX1 DELTEX HOMOLOG 1; HDX-1. [RefSeq;Acc:NM_004416] 0.351313617
0.50755 2251 0.113261 GPD2 "GLYCEROL-3-PHOSPHATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.99.5) (GPD-M) (GPDH-M). [SWISSPROT;Acc:P43304]" 0.223152399
0.508241 1155 0.126888 PAPLN 0.249661086
0.509096 1524 0.123369 RRM1 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M1 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE LARGE CHAIN). [SWISSPROT;Acc:P23921] 0.242329541
0.509937 1465 0.12393 SPO11 MEIOTIC RECOMBINATION PROTEIN SPO11. [SWISSPROT;Acc:Q9Y5K1] 0.243030021
0.510598 2960 0.0746316 no value RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211] 0.146165085
0.511852 448 0.141581 SEC16A 0.276605347
0.512059 1161 0.127791 no value ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1B SUBUNIT (SIGMA-ADAPTIN 1B) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1B SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1B SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1B SMALL CHAIN) (SIGMA 1B SUBUNIT OF AP-1 CL 0.249563039
0.513743 2806 0.101567 ZBTB20 ZINC FINGER PROTEIN 288 (DENDRITIC-DERIVED BTB/POZ ZINC FINGER PROTEIN). [SWISSPROT;Acc:Q9HC78] 0.197700017
0.514211 1645 0.122909 RAD23B UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG B (HHR23B) (XP-C REPAIR COMPLEMENTING COMPLEX 58 KDA PROTEIN) (P58). [SWISSPROT;Acc:P54727] 0.239024447
0.514239 2409 0.112482 no value 0.218734868
0.514271 916 0.132652 VPS33A VACUOLAR PROTEIN SORTING 33A (HVPS33A). [SWISSPROT;Acc:Q96AX1] 0.257941824
0.514373 2807 0.101691 no value 0.197698946
0.514942 2846 0.0987604 ACP1 "RED CELL ACID PHOSPHATASE 1, ISOZYME F (EC 3.1.3.2) (ACP1) (LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE) (EC 3.1.3.48) (ADIPOCYTE ACID PHOSPHATASE, ISOZYME ALPHA). [SWISSPROT;Acc:P24666]" 0.191789367
0.514965 948 0.13204 RABAC1 RAB ACCEPTOR 1 (PRENYLATED); PRENYLATED RAB ACCEPTOR 1. [RefSeq;Acc:NM_006423] 0.256405775
0.51515 1002 0.131317 FH "FUMARATE HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.2) (FUMARASE). [SWISSPROT;Acc:P07954]" 0.25491022
0.515188 2889 0.0926874 C9orf95 0.179909858
0.517345 3069 0.0533885 no value 0.103197093
0.517346 236 0.162809 RANBP5 IMPORTIN BETA-3 SUBUNIT (KARYOPHERIN BETA-3 SUBUNIT) (RAN-BINDING PROTEIN 5). [SWISSPROT;Acc:O00410] 0.314700413
0.517492 2687 0.107786 EHD3 EH-DOMAIN CONTAINING PROTEIN 3. [SWISSPROT;Acc:Q9NZN3] 0.208285345
0.517633 1233 0.128218 PBRM1 POLYBROMO 1. [RefSeq;Acc:NM_018165] 0.247700591
0.517685 3183 0.0257685 PSEN2 PRESENILIN 2 (PS-2) (STM-2) (E5-1) (AD3LP) (AD5). [SWISSPROT;Acc:P49810] 0.049776408
0.518618 1129 0.129983 TYR TYROSINASE PRECURSOR (EC 1.14.18.1) (MONOPHENOL MONOOXYGENASE) (TUMOR REJECTION ANTIGEN AB) (SK29-AB) (LB24-AB). [SWISSPROT;Acc:P14679] 0.250633414
0.519559 2289 0.11552 MAP3K7IP2 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 2 ISOFORM 1; TAK1-BINDING PROTEIN 2. [RefSeq;Acc:NM_015093] 0.22234241
0.519607 83 0.204365 E2F2 TRANSCRIPTION FACTOR E2F2 (E2F-2). [SWISSPROT;Acc:Q14209] 0.393306865
0.522903 2230 0.117296 MLH3 DNA MISMATCH REPAIR PROTEIN MLH3 (MUTL PROTEIN HOMOLOG 3). [SWISSPROT;Acc:Q9UHC1] 0.224316938
0.523598 76 0.212647 C22orf9 0.406126456
0.524421 190 0.17117 BCAR1 CRK-ASSOCIATED SUBSTRATE (P130CAS) (BREAST CANCER ANTI-ESTROGEN RESISTANCE 1 PROTEIN). [SWISSPROT;Acc:P56945] 0.326398066
0.524861 689 0.139426 CAMK2G CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN (EC 2.7.1.123) (CAM-KINASE II GAMMA CHAIN) (CAM KINASE II GAMMA SUBUNIT) (CAMK-II GAMMA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q13555] 0.265643666
0.525053 2725 0.10808 no value 0.205845886
0.525483 523 0.142881 GBE1 "1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC 2.4.1.18) (GLYCOGEN BRANCHING ENZYME) (BRANCHER ENZYME). [SWISSPROT;Acc:Q04446]" 0.271904134
0.525788 1205 0.130571 ZNF593 ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 0.248333929
0.525864 1453 0.127901 UTP18 0.243220681
0.526194 108 0.192957 SCP2 "NONSPECIFIC LIPID-TRANSFER PROTEIN, MITOCHONDRIAL PRECURSOR (NSL-TP) (STEROL CARRIER PROTEIN 2) (SCP-2) (STEROL CARRIER PROTEIN X) (SCP-X) (SCPX). [SWISSPROT;Acc:P22307]" 0.366703155
0.526678 1234 0.130458 SMARCA2 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2 (SNF2-ALPHA). [SWISSPROT;Acc:P51531] 0.247699733
1235 SMARCA4 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L4 (SNF2-BETA) (BRG-1 PROTEIN) (MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR) (BRAHMA PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P51532]
0.526818 952 0.135079 YIF1B SIMILAR TO PUTATIVE TRANSMEMBRANE PROTEIN; HOMOLOG OF YEAST GOLGI MEMBRANE PROTEIN YIF1P (YIP1P-INTERACTING FACTOR). [RefSeq;Acc:NM_033557] 0.256405438
0.527051 1287 0.129655 no value GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [SWISSPROT;Acc:P36915] 0.246000861
0.527101 2513 0.113204 LIMS1 PINCH PROTEIN (PARTICULARLY INTERESTING NEW CYS-HIS PROTEIN) (LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 1). [SWISSPROT;Acc:P48059] 0.214767189
0.528466 2942 0.0819552 NUBP1 NUCLEOTIDE-BINDING PROTEIN 1 (NBP 1). [SWISSPROT;Acc:P53384] 0.155081311
2943 NUBP2 NUCLEOTIDE BINDING PROTEIN 2 (NBP 2). [SWISSPROT;Acc:Q9Y5Y2]
0.528749 2263 0.11794 PRSS12 NEUROTRYPSIN PRECURSOR (EC 3.4.21.-) (MOTOPSIN) (LEYDIN). [SWISSPROT;Acc:P56730] 0.223054795
0.529029 2936 0.0831672 VPS37C 0.157207261

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/