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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
final measured expected Gene Hugo Rank description
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
final
measured
expected
Hugo
Rank
description
0.000219976 0.000173011 0.7865 no value 3206
0.000571223 2.59675 C1orf166 3205
0.000219977 0.000178236 0.81025 no value 3204 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915]
0.023892231 0.0426192 1.78381 RRAGB 3203 RAS-RELATED GTP BINDING B SHORT ISOFORM; GTP-BINDING PROTEIN RAGB. [RefSeq;Acc:NM_006064]
0.023892241 0.0289077 1.20992 ANLN 3202 "ANILLIN, ACTIN BINDING PROTEIN (SCRAPS HOMOLOG, DROSOPHILA); ANILLIN (DROSOPHILA SCRAPS HOMOLOG), ACTIN BINDING PROTEIN. [RefSeq;Acc:NM_018685]"
0.023892303 0.029 1.21378 RRAGC 3201 RAS-RELATED GTP BINDING C; RAG C PROTEIN. [RefSeq;Acc:NM_022157]
0.023892334 0.0391808 1.63989 RRAGA 3200 RAS-RELATED GTP BINDING A; RAS-RELATED GTP-BINDING PROTEIN. [RefSeq;Acc:NM_006570]
0.036862138 0.00386024 0.104721 CHMP2B 3199
0.036862149 0.0100954 0.273869 CHMP2A 3198 PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [RefSeq;Acc:NM_014453]
0.036862168 0.027115 0.735578 VPS24 3197 NEUROENDOCRINE DIFFERENTIATION FACTOR; COMPARATIVE GENE IDENTIFICATION TRANSCRIPT 149. [RefSeq;Acc:NM_016079]
0.036862209 0.031557 0.85608 CHMP4B 3196
0.036862223 0.0179282 0.486357 STAMBP 3195 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM. [RefSeq;Acc:NM_006463]
0.036862264 0.0239451 0.649583 CHMP4C 3194
0.036862282 0.0228851 0.620827 CHMP4A 3193 PROTEIN HSPC134 (PROTEIN CDA04). [SWISSPROT;Acc:Q9BY43]
0.03686237 0.0142939 0.387764 STAMBPL1 3192 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH) LIKE PROTEIN. [RefSeq;Acc:NM_020799]
0.037314982 0.05032 1.34852 FIBCD1 3191
0.037315011 0.0229678 0.615511 PPP1R14D 3190 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 14D; PKC-DEPENDENT PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_017726]"
0.037315028 0.0318436 0.853372 MFAP4 3189 MICROFIBRIL-ASSOCIATED GLYCOPROTEIN 4 PRECURSOR. [SWISSPROT;Acc:P55083]
0.037315104 0.0241928 0.648338 PPP1R14A 3188 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14A; 17-KDA PKC-POTENTIATED INHIBITORY PROTEIN OF PP1. [RefSeq;Acc:NM_033256]"
0.037315105 0.028817 0.772261 no value 3187 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]"
0.037315127 0.0311291 0.834222 FCN2 3186 FICOLIN 2 PRECURSOR (COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2) (FICOLIN-B) (FICOLIN B) (SERUM LECTIN P35) (EBP-37) (HUCOLIN) (L- FICOLIN). [SWISSPROT;Acc:Q15485]
0.04678744 0.0476371 1.01816 CCDC104 3185
0.049410892 0.0656147 1.32794 PYCRL 3184
0.049776408 0.0257685 0.517685 PSEN2 3183 PRESENILIN 2 (PS-2) (STM-2) (E5-1) (AD3LP) (AD5). [SWISSPROT;Acc:P49810]
0.04977643 0.0883895 1.77573 FBXW7 3182 "F-BOX PROTEIN FBW7 ISOFORM 2; ARCHIPELAGO, DROSOPHILA, HOMOLOG OF; F-BOX PROTEIN FBW7; F-BOX PROTEIN SEL-10; HOMOLOG OF C ELEGANS SEL-10. [RefSeq;Acc:NM_018315]"
0.049776476 0.0241952 0.486077 CUL2 3181 CULLIN HOMOLOG 2 (CUL-2). [SWISSPROT;Acc:Q13617]
0.049776478 0.0313105 0.629022 CUL1 3179 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616]
PSEN1 3180 PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768]
0.049776531 0.145007 2.91316 SKP1A 3178 S-PHASE KINASE-ASSOCIATED PROTEIN 1A (CYCLIN A/CDK2-ASSOCIATED PROTEIN P19) (P19A) (P19SKP1) (RNA POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN) (ORGAN OF CORTI PROTEIN 2) (OCP-II PROTEIN) (OCP-2) (TRANSCRIPTION ELONGATION FACTOR B) (SIII). [SWISSPR
0.055311655 0.0184372 0.333333 C6orf130 3176
NIPA2 3175
UBAC1 3177 PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [RefSeq;Acc:NM_016172]
0.055466395 0.0455028 0.820367 NXF5 3174 NUCLEAR RNA EXPORT FACTOR 5 (TAP-LIKE PROTEIN 1) (TAPL-1). [SWISSPROT;Acc:Q9H1B4]
0.055483206 0.0469672 0.846512 NXF3 3173 NUCLEAR RNA EXPORT FACTOR 3 (TAP-LIKE PROTEIN 3) (TAPL-3). [SWISSPROT;Acc:Q9H4D5]
0.055582704 0.057781 1.03955 NXF1 3172 NUCLEAR RNA EXPORT FACTOR 1 (TIP ASSOCIATING PROTEIN) (TIP-ASSOCIATED PROTEIN) (MRNA EXPORT FACTOR TAP). [SWISSPROT;Acc:Q9UBU9]
0.05906224 0.0439931 0.74486 PROSC 3171 PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN. [SWISSPROT;Acc:O94903]
0.059152434 0.0287078 0.485319 CCT3 3170 "T-COMPLEX PROTEIN 1, GAMMA SUBUNIT (TCP-1-GAMMA) (CCT-GAMMA). [SWISSPROT;Acc:P49368]"
0.062788394 0.038917 0.619812 no value 3169 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464]
0.062788507 0.0509886 0.812069 RPS6KC1 3168 "RIBOSOMAL PROTEIN S6 KINASE, 52KDA, POLYPEPTIDE 1; RIBOSOMAL PROTEIN S6 KINASE, 52KD, POLYPEPTIDE 1. [RefSeq;Acc:NM_012424]"
0.06471012 0.73655 11.3823 C5orf33 3167
0.064710168 0.081705 1.26263 no value 3166 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]"
0.06471026 0.0736571 1.13826 MYH4 3165 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, FETAL (MYOSIN HEAVY CHAIN IIB) (MYHC-IIB). [SWISSPROT;Acc:Q9Y623]"
0.064710271 0.0739839 1.14331 MYH2 3164 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 2 (MYOSIN HEAVY CHAIN IIA) (MYHC-IIA). [SWISSPROT;Acc:Q9UKX2]"
0.064710307 0.0816437 1.26168 no value 3163 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]"
0.0647104 0.0727992 1.125 MYH3 3162 "MYOSIN HEAVY CHAIN, FAST SKELETAL MUSCLE, EMBRYONIC (MUSCLE EMBRYONIC MYOSIN HEAVY CHAIN) (SMHCE). [SWISSPROT;Acc:P11055]"
0.064710416 0.0720434 1.11332 MYH13 3161 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, EXTRAOCULAR (MYHC-EO). [SWISSPROT;Acc:Q9UKX3]"
0.064710438 0.0681828 1.05366 MYH7B 3160 DJ756N5.1.1 (CONTINUES IN EM:AL133324 AS DJ1161H23.3) (FRAGMENT). [SPTREMBL;Acc:Q9H430]
0.064710558 0.0736775 1.13857 MYH8 3159 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, PERINATAL (MYHC-PERINATAL). [SWISSPROT;Acc:P13535]"
0.064710559 0.0741473 1.14583 MYH1 3158 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, ADULT 1 (MYOSIN HEAVY CHAIN IIX/D) (MYHC-IIX/D). [SWISSPROT;Acc:P12882]"
0.06503744 0.131587 2.02325 PYCR2 3157 PYRROLINE 5-CARBOXYLATE REDUCTASE ISOFORM. [RefSeq;Acc:NM_013328]

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/